Protein
Design novel protein binders, redesign selected residues in fixed structures, and screen protein libraries against targets.
ProteinDesign
Generate novel protein binders optimized for binding to a target structure. Binder specifications can be provided directly, uploaded as structure templates, or selected from Boltz-managed curated nanobody and antibody defaults. Results are scored by binding confidence (likelihood of protein-protein interaction) and structure confidence.
Start a protein de novo design run
List protein design runs
List curated protein design specifications
Get protein design run status
Get generated protein designs
Stop a running protein design run
Resume a stopped protein design run
Delete protein design run data
Estimate cost for a protein design run
ModelsExpand Collapse
DesignStartResponse object { id, completed_at, created_at, 14 more } A protein design pipeline run that generates novel protein binders
A protein design pipeline run that generates novel protein binders
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
input: object { binder_specification, num_proteins, target, 2 more } Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
binder_specification: object { chain_selection, modality, structure, 2 more } or object { entities, modality, type, 2 more } or object { binder, type, rules } or object { binder_specifications, type } Binder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, boltz_curated for Boltz-managed nanobody and antibody defaults, or uniformly_sampled_specifications to sample uniformly across multiple binder specifications.
Binder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, boltz_curated for Boltz-managed nanobody and antibody defaults, or uniformly_sampled_specifications to sample uniformly across multiple binder specifications.
StructureTemplateBinderSpecResponse object { chain_selection, modality, structure, 2 more } Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
chain_selection: map[object { chain_type, crop_residues, design_motifs } or object { chain_type } ]Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
StructureTemplatePolymerChainSpec object { chain_type, crop_residues, design_motifs } Per-chain crop and design specification for a polymer chain in structure_template mode.
Per-chain crop and design specification for a polymer chain in structure_template mode.
crop_residues: array of number or "all"0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
design_motifs: optional array of object { design_length_range, end_index, start_index, type } or object { after_residue_index, design_length_range, type } Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
ReplacementMotif object { design_length_range, end_index, start_index, type } Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
InsertionMotif object { after_residue_index, design_length_range, type } Insert a designed segment at a specific position in the sequence.
Insert a designed segment at a specific position in the sequence.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
NoTemplateBinderSpecResponse object { entities, modality, type, 2 more } Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 3 moreBinder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
Binder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
DesignedProteinEntityResponse object { chain_ids, type, value, 2 more } Protein binder entity with designed and/or fixed segments.
Protein binder entity with designed and/or fixed segments.
Binder sequence specification. Fixed amino acids are written as literal single-letter codes. Designed regions are written as a length (fixed) or a length range (min..max). Example: “MKTAYI5..10VKSHFSRQ” means fixed MKTAYI, then 5-10 designed residues, then fixed VKSHFSRQ. “20” means 20 fully designed residues. “ACDE8GHI” means fixed ACDE, then 8 designed residues, then fixed GHI.
FixedProteinEntityResponse object { chain_ids, type, value, 2 more } A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
FixedRnaEntityResponse object { chain_ids, type, value, 2 more }
FixedDnaEntityResponse object { chain_ids, type, value, 2 more }
bonds: optional array of object { atom1, atom2 } Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
BoltzCuratedBinderSpecResponse object { binder, type, rules } Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
binder: "boltz_nanobody" or "boltz_antibody"Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
UniformlySampledBinderSpecResponse object { binder_specifications, type } A collection of binder specifications sampled uniformly during protein design. This lets one run explore multiple binder definitions while keeping each generation request shape unchanged.
A collection of binder specifications sampled uniformly during protein design. This lets one run explore multiple binder definitions while keeping each generation request shape unchanged.
binder_specifications: array of object { chain_selection, modality, structure, 2 more } or object { entities, modality, type, 2 more } or object { binder, type, rules } Binder specifications to sample uniformly when generating designs. Each generation samples one specification from this list; over larger runs this gives roughly equal representation.
Binder specifications to sample uniformly when generating designs. Each generation samples one specification from this list; over larger runs this gives roughly equal representation.
StructureTemplateBinderSpecResponse object { chain_selection, modality, structure, 2 more } Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
chain_selection: map[object { chain_type, crop_residues, design_motifs } or object { chain_type } ]Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
StructureTemplatePolymerChainSpec object { chain_type, crop_residues, design_motifs } Per-chain crop and design specification for a polymer chain in structure_template mode.
Per-chain crop and design specification for a polymer chain in structure_template mode.
crop_residues: array of number or "all"0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
design_motifs: optional array of object { design_length_range, end_index, start_index, type } or object { after_residue_index, design_length_range, type } Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
ReplacementMotif object { design_length_range, end_index, start_index, type } Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
InsertionMotif object { after_residue_index, design_length_range, type } Insert a designed segment at a specific position in the sequence.
Insert a designed segment at a specific position in the sequence.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
NoTemplateBinderSpecResponse object { entities, modality, type, 2 more } Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 3 moreBinder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
Binder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
DesignedProteinEntityResponse object { chain_ids, type, value, 2 more } Protein binder entity with designed and/or fixed segments.
Protein binder entity with designed and/or fixed segments.
Binder sequence specification. Fixed amino acids are written as literal single-letter codes. Designed regions are written as a length (fixed) or a length range (min..max). Example: “MKTAYI5..10VKSHFSRQ” means fixed MKTAYI, then 5-10 designed residues, then fixed VKSHFSRQ. “20” means 20 fully designed residues. “ACDE8GHI” means fixed ACDE, then 8 designed residues, then fixed GHI.
FixedProteinEntityResponse object { chain_ids, type, value, 2 more } A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
FixedRnaEntityResponse object { chain_ids, type, value, 2 more }
FixedDnaEntityResponse object { chain_ids, type, value, 2 more }
bonds: optional array of object { atom1, atom2 } Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
BoltzCuratedBinderSpecResponse object { binder, type, rules } Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
binder: "boltz_nanobody" or "boltz_antibody"Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
Number of protein designs to generate. Must be between 10 and 1,000,000.
target: object { chain_selection, structure, type } or object { entities, type, bonds, 4 more } Target specification (structure template or template-free)
Target specification (structure template or template-free)
StructureTemplateTargetResponse object { chain_selection, structure, type } Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
chain_selection: map[object { chain_type, crop_residues, epitope_residues, 2 more } or object { chain_type } ]Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
StructureTemplateTargetPolymerChainSpec object { chain_type, crop_residues, epitope_residues, 2 more } Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
crop_residues: array of number or "all"0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices where binder contact is desired (the epitope). All indices must be present in crop_residues and must not overlap non_binding_residues.
NoTemplateTargetResponse object { entities, type, bonds, 4 more } Target defined by sequences only, without a 3D structure template
Target defined by sequences only, without a 3D structure template
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 2 moreEntities (proteins, RNA, DNA, ligands) defining the target complex.
Entities (proteins, RNA, DNA, ligands) defining the target complex.
ProteinEntityResponse object { chain_ids, type, value, 2 more }
RnaEntityResponse object { chain_ids, type, value, 2 more }
DnaEntityResponse object { chain_ids, type, value, 2 more }
bonds: optional array of object { atom1, atom2 } Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
constraints: optional array of object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } or object { max_distance_angstrom, token1, token2, 2 more } Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
PocketConstraintResponse object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } Constrains the binder to interact with specific pocket residues on the target.
Constrains the binder to interact with specific pocket residues on the target.
Binding pocket residues keyed by chain ID. Each key is a chain ID (e.g. “A”) and the value is an array of 0-indexed residue indices that define the pocket on that chain.
ContactConstraintResponse object { max_distance_angstrom, token1, token2, 2 more } Maximum-distance contact constraint between two polymer residues or ligand atoms.
Maximum-distance contact constraint between two polymer residues or ligand atoms.
token1: object { chain_id, residue_index, type } or object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandContactTokenResponse object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
token2: object { chain_id, residue_index, type } or object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandContactTokenResponse object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).
DesignListResponse object { id, completed_at, created_at, 13 more } Summary of a protein design pipeline run (excludes input)
Summary of a protein design pipeline run (excludes input)
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
DesignListCuratedSpecificationsResponse object { data }
data: array of object { binder_specification, name }
binder_specification: object { chain_selection, modality, structure, 2 more } or object { entities, modality, type, 2 more } or object { binder, type, rules } or object { binder_specifications, type } Binder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, boltz_curated for Boltz-managed nanobody and antibody defaults, or uniformly_sampled_specifications to sample uniformly across multiple binder specifications.
Binder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, boltz_curated for Boltz-managed nanobody and antibody defaults, or uniformly_sampled_specifications to sample uniformly across multiple binder specifications.
StructureTemplateBinderSpec object { chain_selection, modality, structure, 2 more } Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
chain_selection: map[object { chain_type, crop_residues, design_motifs } or object { chain_type } ]Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
StructureTemplatePolymerChainSpec object { chain_type, crop_residues, design_motifs } Per-chain crop and design specification for a polymer chain in structure_template mode.
Per-chain crop and design specification for a polymer chain in structure_template mode.
crop_residues: array of number or "all"0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
design_motifs: optional array of object { design_length_range, end_index, start_index, type } or object { after_residue_index, design_length_range, type } Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
ReplacementMotif object { design_length_range, end_index, start_index, type } Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
InsertionMotif object { after_residue_index, design_length_range, type } Insert a designed segment at a specific position in the sequence.
Insert a designed segment at a specific position in the sequence.
structure: object { type, url } or object { data, media_type, type } How to provide a CIF structure file. URLs are auto-detected; base64 uploads must use chemical/x-cif media type.
How to provide a CIF structure file. URLs are auto-detected; base64 uploads must use chemical/x-cif media type.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
NoTemplateBinderSpec object { entities, modality, type, 2 more } Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 3 moreBinder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
Binder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
DesignedProteinEntity object { chain_ids, type, value, 2 more } Protein binder entity with designed and/or fixed segments.
Protein binder entity with designed and/or fixed segments.
Binder sequence specification. Fixed amino acids are written as literal single-letter codes. Designed regions are written as a length (fixed) or a length range (min..max). Example: “MKTAYI5..10VKSHFSRQ” means fixed MKTAYI, then 5-10 designed residues, then fixed VKSHFSRQ. “20” means 20 fully designed residues. “ACDE8GHI” means fixed ACDE, then 8 designed residues, then fixed GHI.
FixedProteinEntity object { chain_ids, type, value, 2 more } A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
FixedRnaEntity object { chain_ids, type, value, 2 more }
FixedDnaEntity object { chain_ids, type, value, 2 more }
bonds: optional array of object { atom1, atom2 } Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtom object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtom object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
BoltzCuratedBinderSpec object { binder, type, rules } Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
binder: "boltz_nanobody" or "boltz_antibody"Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
UniformlySampledBinderSpec object { binder_specifications, type } A collection of binder specifications sampled uniformly during protein design. This lets one run explore multiple binder definitions while keeping each generation request shape unchanged.
A collection of binder specifications sampled uniformly during protein design. This lets one run explore multiple binder definitions while keeping each generation request shape unchanged.
binder_specifications: array of object { chain_selection, modality, structure, 2 more } or object { entities, modality, type, 2 more } or object { binder, type, rules } Binder specifications to sample uniformly when generating designs. Each generation samples one specification from this list; over larger runs this gives roughly equal representation.
Binder specifications to sample uniformly when generating designs. Each generation samples one specification from this list; over larger runs this gives roughly equal representation.
StructureTemplateBinderSpec object { chain_selection, modality, structure, 2 more } Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
chain_selection: map[object { chain_type, crop_residues, design_motifs } or object { chain_type } ]Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
StructureTemplatePolymerChainSpec object { chain_type, crop_residues, design_motifs } Per-chain crop and design specification for a polymer chain in structure_template mode.
Per-chain crop and design specification for a polymer chain in structure_template mode.
crop_residues: array of number or "all"0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
design_motifs: optional array of object { design_length_range, end_index, start_index, type } or object { after_residue_index, design_length_range, type } Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
ReplacementMotif object { design_length_range, end_index, start_index, type } Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
InsertionMotif object { after_residue_index, design_length_range, type } Insert a designed segment at a specific position in the sequence.
Insert a designed segment at a specific position in the sequence.
structure: object { type, url } or object { data, media_type, type } How to provide a CIF structure file. URLs are auto-detected; base64 uploads must use chemical/x-cif media type.
How to provide a CIF structure file. URLs are auto-detected; base64 uploads must use chemical/x-cif media type.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
NoTemplateBinderSpec object { entities, modality, type, 2 more } Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 3 moreBinder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
Binder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
DesignedProteinEntity object { chain_ids, type, value, 2 more } Protein binder entity with designed and/or fixed segments.
Protein binder entity with designed and/or fixed segments.
Binder sequence specification. Fixed amino acids are written as literal single-letter codes. Designed regions are written as a length (fixed) or a length range (min..max). Example: “MKTAYI5..10VKSHFSRQ” means fixed MKTAYI, then 5-10 designed residues, then fixed VKSHFSRQ. “20” means 20 fully designed residues. “ACDE8GHI” means fixed ACDE, then 8 designed residues, then fixed GHI.
FixedProteinEntity object { chain_ids, type, value, 2 more } A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
FixedRnaEntity object { chain_ids, type, value, 2 more }
FixedDnaEntity object { chain_ids, type, value, 2 more }
bonds: optional array of object { atom1, atom2 } Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtom object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtom object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
BoltzCuratedBinderSpec object { binder, type, rules } Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
binder: "boltz_nanobody" or "boltz_antibody"Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
DesignRetrieveResponse object { id, completed_at, created_at, 14 more } A protein design pipeline run that generates novel protein binders
A protein design pipeline run that generates novel protein binders
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
input: object { binder_specification, num_proteins, target, 2 more } Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
binder_specification: object { chain_selection, modality, structure, 2 more } or object { entities, modality, type, 2 more } or object { binder, type, rules } or object { binder_specifications, type } Binder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, boltz_curated for Boltz-managed nanobody and antibody defaults, or uniformly_sampled_specifications to sample uniformly across multiple binder specifications.
Binder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, boltz_curated for Boltz-managed nanobody and antibody defaults, or uniformly_sampled_specifications to sample uniformly across multiple binder specifications.
StructureTemplateBinderSpecResponse object { chain_selection, modality, structure, 2 more } Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
chain_selection: map[object { chain_type, crop_residues, design_motifs } or object { chain_type } ]Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
StructureTemplatePolymerChainSpec object { chain_type, crop_residues, design_motifs } Per-chain crop and design specification for a polymer chain in structure_template mode.
Per-chain crop and design specification for a polymer chain in structure_template mode.
crop_residues: array of number or "all"0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
design_motifs: optional array of object { design_length_range, end_index, start_index, type } or object { after_residue_index, design_length_range, type } Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
ReplacementMotif object { design_length_range, end_index, start_index, type } Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
InsertionMotif object { after_residue_index, design_length_range, type } Insert a designed segment at a specific position in the sequence.
Insert a designed segment at a specific position in the sequence.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
NoTemplateBinderSpecResponse object { entities, modality, type, 2 more } Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 3 moreBinder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
Binder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
DesignedProteinEntityResponse object { chain_ids, type, value, 2 more } Protein binder entity with designed and/or fixed segments.
Protein binder entity with designed and/or fixed segments.
Binder sequence specification. Fixed amino acids are written as literal single-letter codes. Designed regions are written as a length (fixed) or a length range (min..max). Example: “MKTAYI5..10VKSHFSRQ” means fixed MKTAYI, then 5-10 designed residues, then fixed VKSHFSRQ. “20” means 20 fully designed residues. “ACDE8GHI” means fixed ACDE, then 8 designed residues, then fixed GHI.
FixedProteinEntityResponse object { chain_ids, type, value, 2 more } A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
FixedRnaEntityResponse object { chain_ids, type, value, 2 more }
FixedDnaEntityResponse object { chain_ids, type, value, 2 more }
bonds: optional array of object { atom1, atom2 } Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
BoltzCuratedBinderSpecResponse object { binder, type, rules } Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
binder: "boltz_nanobody" or "boltz_antibody"Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
UniformlySampledBinderSpecResponse object { binder_specifications, type } A collection of binder specifications sampled uniformly during protein design. This lets one run explore multiple binder definitions while keeping each generation request shape unchanged.
A collection of binder specifications sampled uniformly during protein design. This lets one run explore multiple binder definitions while keeping each generation request shape unchanged.
binder_specifications: array of object { chain_selection, modality, structure, 2 more } or object { entities, modality, type, 2 more } or object { binder, type, rules } Binder specifications to sample uniformly when generating designs. Each generation samples one specification from this list; over larger runs this gives roughly equal representation.
Binder specifications to sample uniformly when generating designs. Each generation samples one specification from this list; over larger runs this gives roughly equal representation.
StructureTemplateBinderSpecResponse object { chain_selection, modality, structure, 2 more } Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
chain_selection: map[object { chain_type, crop_residues, design_motifs } or object { chain_type } ]Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
StructureTemplatePolymerChainSpec object { chain_type, crop_residues, design_motifs } Per-chain crop and design specification for a polymer chain in structure_template mode.
Per-chain crop and design specification for a polymer chain in structure_template mode.
crop_residues: array of number or "all"0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
design_motifs: optional array of object { design_length_range, end_index, start_index, type } or object { after_residue_index, design_length_range, type } Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
ReplacementMotif object { design_length_range, end_index, start_index, type } Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
InsertionMotif object { after_residue_index, design_length_range, type } Insert a designed segment at a specific position in the sequence.
Insert a designed segment at a specific position in the sequence.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
NoTemplateBinderSpecResponse object { entities, modality, type, 2 more } Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 3 moreBinder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
Binder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
DesignedProteinEntityResponse object { chain_ids, type, value, 2 more } Protein binder entity with designed and/or fixed segments.
Protein binder entity with designed and/or fixed segments.
Binder sequence specification. Fixed amino acids are written as literal single-letter codes. Designed regions are written as a length (fixed) or a length range (min..max). Example: “MKTAYI5..10VKSHFSRQ” means fixed MKTAYI, then 5-10 designed residues, then fixed VKSHFSRQ. “20” means 20 fully designed residues. “ACDE8GHI” means fixed ACDE, then 8 designed residues, then fixed GHI.
FixedProteinEntityResponse object { chain_ids, type, value, 2 more } A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
FixedRnaEntityResponse object { chain_ids, type, value, 2 more }
FixedDnaEntityResponse object { chain_ids, type, value, 2 more }
bonds: optional array of object { atom1, atom2 } Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
BoltzCuratedBinderSpecResponse object { binder, type, rules } Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
binder: "boltz_nanobody" or "boltz_antibody"Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
Number of protein designs to generate. Must be between 10 and 1,000,000.
target: object { chain_selection, structure, type } or object { entities, type, bonds, 4 more } Target specification (structure template or template-free)
Target specification (structure template or template-free)
StructureTemplateTargetResponse object { chain_selection, structure, type } Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
chain_selection: map[object { chain_type, crop_residues, epitope_residues, 2 more } or object { chain_type } ]Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
StructureTemplateTargetPolymerChainSpec object { chain_type, crop_residues, epitope_residues, 2 more } Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
crop_residues: array of number or "all"0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices where binder contact is desired (the epitope). All indices must be present in crop_residues and must not overlap non_binding_residues.
NoTemplateTargetResponse object { entities, type, bonds, 4 more } Target defined by sequences only, without a 3D structure template
Target defined by sequences only, without a 3D structure template
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 2 moreEntities (proteins, RNA, DNA, ligands) defining the target complex.
Entities (proteins, RNA, DNA, ligands) defining the target complex.
ProteinEntityResponse object { chain_ids, type, value, 2 more }
RnaEntityResponse object { chain_ids, type, value, 2 more }
DnaEntityResponse object { chain_ids, type, value, 2 more }
bonds: optional array of object { atom1, atom2 } Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
constraints: optional array of object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } or object { max_distance_angstrom, token1, token2, 2 more } Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
PocketConstraintResponse object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } Constrains the binder to interact with specific pocket residues on the target.
Constrains the binder to interact with specific pocket residues on the target.
Binding pocket residues keyed by chain ID. Each key is a chain ID (e.g. “A”) and the value is an array of 0-indexed residue indices that define the pocket on that chain.
ContactConstraintResponse object { max_distance_angstrom, token1, token2, 2 more } Maximum-distance contact constraint between two polymer residues or ligand atoms.
Maximum-distance contact constraint between two polymer residues or ligand atoms.
token1: object { chain_id, residue_index, type } or object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandContactTokenResponse object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
token2: object { chain_id, residue_index, type } or object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandContactTokenResponse object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).
DesignListResultsResponse object { id, artifacts, created_at, 3 more } A single generated protein design
A single generated protein design
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 2 moreEntities in the designed complex, including designed and fixed input entities.
Entities in the designed complex, including designed and fixed input entities.
ProteinEntity object { chain_ids, type, value, 2 more }
RnaEntity object { chain_ids, type, value, 2 more }
DnaEntity object { chain_ids, type, value, 2 more }
metrics: object { binding_confidence, helix_fraction, iptm, 4 more } Structural and binding quality metrics for a designed protein binder
Structural and binding quality metrics for a designed protein binder
Confidence that the designed binder binds the target (0-1). Primary metric for hit discovery.
Fraction of the designed sequence forming alpha helices (0-1).
DesignStopResponse object { id, completed_at, created_at, 14 more } A protein design pipeline run that generates novel protein binders
A protein design pipeline run that generates novel protein binders
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
input: object { binder_specification, num_proteins, target, 2 more } Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
binder_specification: object { chain_selection, modality, structure, 2 more } or object { entities, modality, type, 2 more } or object { binder, type, rules } or object { binder_specifications, type } Binder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, boltz_curated for Boltz-managed nanobody and antibody defaults, or uniformly_sampled_specifications to sample uniformly across multiple binder specifications.
Binder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, boltz_curated for Boltz-managed nanobody and antibody defaults, or uniformly_sampled_specifications to sample uniformly across multiple binder specifications.
StructureTemplateBinderSpecResponse object { chain_selection, modality, structure, 2 more } Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
chain_selection: map[object { chain_type, crop_residues, design_motifs } or object { chain_type } ]Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
StructureTemplatePolymerChainSpec object { chain_type, crop_residues, design_motifs } Per-chain crop and design specification for a polymer chain in structure_template mode.
Per-chain crop and design specification for a polymer chain in structure_template mode.
crop_residues: array of number or "all"0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
design_motifs: optional array of object { design_length_range, end_index, start_index, type } or object { after_residue_index, design_length_range, type } Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
ReplacementMotif object { design_length_range, end_index, start_index, type } Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
InsertionMotif object { after_residue_index, design_length_range, type } Insert a designed segment at a specific position in the sequence.
Insert a designed segment at a specific position in the sequence.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
NoTemplateBinderSpecResponse object { entities, modality, type, 2 more } Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 3 moreBinder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
Binder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
DesignedProteinEntityResponse object { chain_ids, type, value, 2 more } Protein binder entity with designed and/or fixed segments.
Protein binder entity with designed and/or fixed segments.
Binder sequence specification. Fixed amino acids are written as literal single-letter codes. Designed regions are written as a length (fixed) or a length range (min..max). Example: “MKTAYI5..10VKSHFSRQ” means fixed MKTAYI, then 5-10 designed residues, then fixed VKSHFSRQ. “20” means 20 fully designed residues. “ACDE8GHI” means fixed ACDE, then 8 designed residues, then fixed GHI.
FixedProteinEntityResponse object { chain_ids, type, value, 2 more } A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
FixedRnaEntityResponse object { chain_ids, type, value, 2 more }
FixedDnaEntityResponse object { chain_ids, type, value, 2 more }
bonds: optional array of object { atom1, atom2 } Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
BoltzCuratedBinderSpecResponse object { binder, type, rules } Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
binder: "boltz_nanobody" or "boltz_antibody"Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
UniformlySampledBinderSpecResponse object { binder_specifications, type } A collection of binder specifications sampled uniformly during protein design. This lets one run explore multiple binder definitions while keeping each generation request shape unchanged.
A collection of binder specifications sampled uniformly during protein design. This lets one run explore multiple binder definitions while keeping each generation request shape unchanged.
binder_specifications: array of object { chain_selection, modality, structure, 2 more } or object { entities, modality, type, 2 more } or object { binder, type, rules } Binder specifications to sample uniformly when generating designs. Each generation samples one specification from this list; over larger runs this gives roughly equal representation.
Binder specifications to sample uniformly when generating designs. Each generation samples one specification from this list; over larger runs this gives roughly equal representation.
StructureTemplateBinderSpecResponse object { chain_selection, modality, structure, 2 more } Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
chain_selection: map[object { chain_type, crop_residues, design_motifs } or object { chain_type } ]Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
StructureTemplatePolymerChainSpec object { chain_type, crop_residues, design_motifs } Per-chain crop and design specification for a polymer chain in structure_template mode.
Per-chain crop and design specification for a polymer chain in structure_template mode.
crop_residues: array of number or "all"0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
design_motifs: optional array of object { design_length_range, end_index, start_index, type } or object { after_residue_index, design_length_range, type } Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
ReplacementMotif object { design_length_range, end_index, start_index, type } Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
InsertionMotif object { after_residue_index, design_length_range, type } Insert a designed segment at a specific position in the sequence.
Insert a designed segment at a specific position in the sequence.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
NoTemplateBinderSpecResponse object { entities, modality, type, 2 more } Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 3 moreBinder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
Binder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
DesignedProteinEntityResponse object { chain_ids, type, value, 2 more } Protein binder entity with designed and/or fixed segments.
Protein binder entity with designed and/or fixed segments.
Binder sequence specification. Fixed amino acids are written as literal single-letter codes. Designed regions are written as a length (fixed) or a length range (min..max). Example: “MKTAYI5..10VKSHFSRQ” means fixed MKTAYI, then 5-10 designed residues, then fixed VKSHFSRQ. “20” means 20 fully designed residues. “ACDE8GHI” means fixed ACDE, then 8 designed residues, then fixed GHI.
FixedProteinEntityResponse object { chain_ids, type, value, 2 more } A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
FixedRnaEntityResponse object { chain_ids, type, value, 2 more }
FixedDnaEntityResponse object { chain_ids, type, value, 2 more }
bonds: optional array of object { atom1, atom2 } Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
BoltzCuratedBinderSpecResponse object { binder, type, rules } Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
binder: "boltz_nanobody" or "boltz_antibody"Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
Number of protein designs to generate. Must be between 10 and 1,000,000.
target: object { chain_selection, structure, type } or object { entities, type, bonds, 4 more } Target specification (structure template or template-free)
Target specification (structure template or template-free)
StructureTemplateTargetResponse object { chain_selection, structure, type } Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
chain_selection: map[object { chain_type, crop_residues, epitope_residues, 2 more } or object { chain_type } ]Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
StructureTemplateTargetPolymerChainSpec object { chain_type, crop_residues, epitope_residues, 2 more } Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
crop_residues: array of number or "all"0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices where binder contact is desired (the epitope). All indices must be present in crop_residues and must not overlap non_binding_residues.
NoTemplateTargetResponse object { entities, type, bonds, 4 more } Target defined by sequences only, without a 3D structure template
Target defined by sequences only, without a 3D structure template
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 2 moreEntities (proteins, RNA, DNA, ligands) defining the target complex.
Entities (proteins, RNA, DNA, ligands) defining the target complex.
ProteinEntityResponse object { chain_ids, type, value, 2 more }
RnaEntityResponse object { chain_ids, type, value, 2 more }
DnaEntityResponse object { chain_ids, type, value, 2 more }
bonds: optional array of object { atom1, atom2 } Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
constraints: optional array of object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } or object { max_distance_angstrom, token1, token2, 2 more } Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
PocketConstraintResponse object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } Constrains the binder to interact with specific pocket residues on the target.
Constrains the binder to interact with specific pocket residues on the target.
Binding pocket residues keyed by chain ID. Each key is a chain ID (e.g. “A”) and the value is an array of 0-indexed residue indices that define the pocket on that chain.
ContactConstraintResponse object { max_distance_angstrom, token1, token2, 2 more } Maximum-distance contact constraint between two polymer residues or ligand atoms.
Maximum-distance contact constraint between two polymer residues or ligand atoms.
token1: object { chain_id, residue_index, type } or object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandContactTokenResponse object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
token2: object { chain_id, residue_index, type } or object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandContactTokenResponse object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).
DesignResumeResponse object { id, completed_at, created_at, 14 more } A protein design pipeline run that generates novel protein binders
A protein design pipeline run that generates novel protein binders
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
input: object { binder_specification, num_proteins, target, 2 more } Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
binder_specification: object { chain_selection, modality, structure, 2 more } or object { entities, modality, type, 2 more } or object { binder, type, rules } or object { binder_specifications, type } Binder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, boltz_curated for Boltz-managed nanobody and antibody defaults, or uniformly_sampled_specifications to sample uniformly across multiple binder specifications.
Binder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, boltz_curated for Boltz-managed nanobody and antibody defaults, or uniformly_sampled_specifications to sample uniformly across multiple binder specifications.
StructureTemplateBinderSpecResponse object { chain_selection, modality, structure, 2 more } Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
chain_selection: map[object { chain_type, crop_residues, design_motifs } or object { chain_type } ]Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
StructureTemplatePolymerChainSpec object { chain_type, crop_residues, design_motifs } Per-chain crop and design specification for a polymer chain in structure_template mode.
Per-chain crop and design specification for a polymer chain in structure_template mode.
crop_residues: array of number or "all"0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
design_motifs: optional array of object { design_length_range, end_index, start_index, type } or object { after_residue_index, design_length_range, type } Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
ReplacementMotif object { design_length_range, end_index, start_index, type } Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
InsertionMotif object { after_residue_index, design_length_range, type } Insert a designed segment at a specific position in the sequence.
Insert a designed segment at a specific position in the sequence.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
NoTemplateBinderSpecResponse object { entities, modality, type, 2 more } Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 3 moreBinder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
Binder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
DesignedProteinEntityResponse object { chain_ids, type, value, 2 more } Protein binder entity with designed and/or fixed segments.
Protein binder entity with designed and/or fixed segments.
Binder sequence specification. Fixed amino acids are written as literal single-letter codes. Designed regions are written as a length (fixed) or a length range (min..max). Example: “MKTAYI5..10VKSHFSRQ” means fixed MKTAYI, then 5-10 designed residues, then fixed VKSHFSRQ. “20” means 20 fully designed residues. “ACDE8GHI” means fixed ACDE, then 8 designed residues, then fixed GHI.
FixedProteinEntityResponse object { chain_ids, type, value, 2 more } A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
FixedRnaEntityResponse object { chain_ids, type, value, 2 more }
FixedDnaEntityResponse object { chain_ids, type, value, 2 more }
bonds: optional array of object { atom1, atom2 } Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
BoltzCuratedBinderSpecResponse object { binder, type, rules } Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
binder: "boltz_nanobody" or "boltz_antibody"Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
UniformlySampledBinderSpecResponse object { binder_specifications, type } A collection of binder specifications sampled uniformly during protein design. This lets one run explore multiple binder definitions while keeping each generation request shape unchanged.
A collection of binder specifications sampled uniformly during protein design. This lets one run explore multiple binder definitions while keeping each generation request shape unchanged.
binder_specifications: array of object { chain_selection, modality, structure, 2 more } or object { entities, modality, type, 2 more } or object { binder, type, rules } Binder specifications to sample uniformly when generating designs. Each generation samples one specification from this list; over larger runs this gives roughly equal representation.
Binder specifications to sample uniformly when generating designs. Each generation samples one specification from this list; over larger runs this gives roughly equal representation.
StructureTemplateBinderSpecResponse object { chain_selection, modality, structure, 2 more } Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
chain_selection: map[object { chain_type, crop_residues, design_motifs } or object { chain_type } ]Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
StructureTemplatePolymerChainSpec object { chain_type, crop_residues, design_motifs } Per-chain crop and design specification for a polymer chain in structure_template mode.
Per-chain crop and design specification for a polymer chain in structure_template mode.
crop_residues: array of number or "all"0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
design_motifs: optional array of object { design_length_range, end_index, start_index, type } or object { after_residue_index, design_length_range, type } Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
ReplacementMotif object { design_length_range, end_index, start_index, type } Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
InsertionMotif object { after_residue_index, design_length_range, type } Insert a designed segment at a specific position in the sequence.
Insert a designed segment at a specific position in the sequence.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
NoTemplateBinderSpecResponse object { entities, modality, type, 2 more } Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 3 moreBinder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
Binder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
DesignedProteinEntityResponse object { chain_ids, type, value, 2 more } Protein binder entity with designed and/or fixed segments.
Protein binder entity with designed and/or fixed segments.
Binder sequence specification. Fixed amino acids are written as literal single-letter codes. Designed regions are written as a length (fixed) or a length range (min..max). Example: “MKTAYI5..10VKSHFSRQ” means fixed MKTAYI, then 5-10 designed residues, then fixed VKSHFSRQ. “20” means 20 fully designed residues. “ACDE8GHI” means fixed ACDE, then 8 designed residues, then fixed GHI.
FixedProteinEntityResponse object { chain_ids, type, value, 2 more } A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
FixedRnaEntityResponse object { chain_ids, type, value, 2 more }
FixedDnaEntityResponse object { chain_ids, type, value, 2 more }
bonds: optional array of object { atom1, atom2 } Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
BoltzCuratedBinderSpecResponse object { binder, type, rules } Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
binder: "boltz_nanobody" or "boltz_antibody"Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction } Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
Number of protein designs to generate. Must be between 10 and 1,000,000.
target: object { chain_selection, structure, type } or object { entities, type, bonds, 4 more } Target specification (structure template or template-free)
Target specification (structure template or template-free)
StructureTemplateTargetResponse object { chain_selection, structure, type } Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
chain_selection: map[object { chain_type, crop_residues, epitope_residues, 2 more } or object { chain_type } ]Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
StructureTemplateTargetPolymerChainSpec object { chain_type, crop_residues, epitope_residues, 2 more } Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
crop_residues: array of number or "all"0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices where binder contact is desired (the epitope). All indices must be present in crop_residues and must not overlap non_binding_residues.
NoTemplateTargetResponse object { entities, type, bonds, 4 more } Target defined by sequences only, without a 3D structure template
Target defined by sequences only, without a 3D structure template
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 2 moreEntities (proteins, RNA, DNA, ligands) defining the target complex.
Entities (proteins, RNA, DNA, ligands) defining the target complex.
ProteinEntityResponse object { chain_ids, type, value, 2 more }
RnaEntityResponse object { chain_ids, type, value, 2 more }
DnaEntityResponse object { chain_ids, type, value, 2 more }
bonds: optional array of object { atom1, atom2 } Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
constraints: optional array of object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } or object { max_distance_angstrom, token1, token2, 2 more } Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
PocketConstraintResponse object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } Constrains the binder to interact with specific pocket residues on the target.
Constrains the binder to interact with specific pocket residues on the target.
Binding pocket residues keyed by chain ID. Each key is a chain ID (e.g. “A”) and the value is an array of 0-indexed residue indices that define the pocket on that chain.
ContactConstraintResponse object { max_distance_angstrom, token1, token2, 2 more } Maximum-distance contact constraint between two polymer residues or ligand atoms.
Maximum-distance contact constraint between two polymer residues or ligand atoms.
token1: object { chain_id, residue_index, type } or object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandContactTokenResponse object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
token2: object { chain_id, residue_index, type } or object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandContactTokenResponse object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).
DesignEstimateCostResponse object { breakdown, disclaimer, estimated_cost_usd } Estimate response with monetary values encoded as decimal strings to preserve precision.
Estimate response with monetary values encoded as decimal strings to preserve precision.
breakdown: object { application, cost_per_unit_usd, num_units } Cost breakdown for the billed application.
Cost breakdown for the billed application.
application: "structure_and_binding" or "small_molecule_design" or "small_molecule_library_screen" or 4 more
ProteinSequence Redesign
Redesign selected protein residues in one fixed CIF structure. Use the top-level type discriminator to choose binder redesign, with target and binder chain roles, or generic redesign. Every chain in the input structure must be assigned exactly once. Binder results include binding and structure metrics; generic results include structure and secondary-structure metrics.
Start a protein sequence redesign run
List protein sequence redesign runs
Get protein sequence redesign run status
Get redesigned protein sequences
Stop a running protein sequence redesign run
Resume a stopped protein sequence redesign run
Delete protein sequence redesign run data
Estimate cost for a protein sequence redesign run
ModelsExpand Collapse
SequenceRedesignStartResponse object { id, completed_at, created_at, 14 more } A fixed-structure protein sequence redesign run.
A fixed-structure protein sequence redesign run.
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
input: object { entities, num_proteins, structure, 4 more } or object { entities, num_proteins, structure, 4 more } Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
BinderProteinSequenceRedesignRunInputResponse object { entities, num_proteins, structure, 4 more }
entities: array of object { chain_id, role, type } or object { chain_id, role, type, design_motifs } Every chain in the input CIF, assigned exactly once as target or binder.
Every chain in the input CIF, assigned exactly once as target or binder.
BinderSequenceRedesignTargetEntityResponse object { chain_id, role, type } A fixed target chain from the input CIF.
A fixed target chain from the input CIF.
BinderSequenceRedesignBinderEntityResponse object { chain_id, role, type, design_motifs }
design_motifs: optional array of object { filters, residues, type } Residues to redesign. Omit this field to keep the binder chain fixed.
Residues to redesign. Omit this field to keep the binder chain fixed.
filters: array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type } Filters applied to this motif in addition to global_design_filters.
Filters applied to this motif in addition to global_design_filters.
Number of unique filter-passing redesigned proteins to generate.
global_design_filters: optional array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type } Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
GenericProteinSequenceRedesignRunInputResponse object { entities, num_proteins, structure, 4 more }
entities: array of object { chain_id, type, design_motifs } Every chain in the input CIF, assigned exactly once.
Every chain in the input CIF, assigned exactly once.
design_motifs: optional array of object { filters, residues, type } Residues to redesign. Omit this field to keep the chain fixed.
Residues to redesign. Omit this field to keep the chain fixed.
filters: array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type } Filters applied to this motif in addition to global_design_filters.
Filters applied to this motif in addition to global_design_filters.
Number of unique filter-passing redesigned proteins to generate.
global_design_filters: optional array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type } Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
SequenceRedesignListResponse object { id, completed_at, created_at, 13 more } Summary of a protein sequence redesign run.
Summary of a protein sequence redesign run.
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
SequenceRedesignRetrieveResponse object { id, completed_at, created_at, 14 more } A fixed-structure protein sequence redesign run.
A fixed-structure protein sequence redesign run.
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
input: object { entities, num_proteins, structure, 4 more } or object { entities, num_proteins, structure, 4 more } Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
BinderProteinSequenceRedesignRunInputResponse object { entities, num_proteins, structure, 4 more }
entities: array of object { chain_id, role, type } or object { chain_id, role, type, design_motifs } Every chain in the input CIF, assigned exactly once as target or binder.
Every chain in the input CIF, assigned exactly once as target or binder.
BinderSequenceRedesignTargetEntityResponse object { chain_id, role, type } A fixed target chain from the input CIF.
A fixed target chain from the input CIF.
BinderSequenceRedesignBinderEntityResponse object { chain_id, role, type, design_motifs }
design_motifs: optional array of object { filters, residues, type } Residues to redesign. Omit this field to keep the binder chain fixed.
Residues to redesign. Omit this field to keep the binder chain fixed.
filters: array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type } Filters applied to this motif in addition to global_design_filters.
Filters applied to this motif in addition to global_design_filters.
Number of unique filter-passing redesigned proteins to generate.
global_design_filters: optional array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type } Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
GenericProteinSequenceRedesignRunInputResponse object { entities, num_proteins, structure, 4 more }
entities: array of object { chain_id, type, design_motifs } Every chain in the input CIF, assigned exactly once.
Every chain in the input CIF, assigned exactly once.
design_motifs: optional array of object { filters, residues, type } Residues to redesign. Omit this field to keep the chain fixed.
Residues to redesign. Omit this field to keep the chain fixed.
filters: array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type } Filters applied to this motif in addition to global_design_filters.
Filters applied to this motif in addition to global_design_filters.
Number of unique filter-passing redesigned proteins to generate.
global_design_filters: optional array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type } Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
SequenceRedesignListResultsResponse = object { id, artifacts, created_at, 4 more } or object { id, artifacts, created_at, 4 more }
BinderProteinDesignResult object { id, artifacts, created_at, 4 more }
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 2 moreEntities in the designed complex, including designed and fixed input entities.
Entities in the designed complex, including designed and fixed input entities.
ProteinEntity object { chain_ids, type, value, 2 more }
RnaEntity object { chain_ids, type, value, 2 more }
DnaEntity object { chain_ids, type, value, 2 more }
metrics: object { binding_confidence, helix_fraction, iptm, 4 more } Structural and binding quality metrics for a designed protein binder
Structural and binding quality metrics for a designed protein binder
Confidence that the designed binder binds the target (0-1). Primary metric for hit discovery.
Fraction of the designed sequence forming alpha helices (0-1).
GenericProteinDesignResult object { id, artifacts, created_at, 4 more }
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 2 moreEntities in the designed complex, including designed and fixed input entities.
Entities in the designed complex, including designed and fixed input entities.
ProteinEntity object { chain_ids, type, value, 2 more }
RnaEntity object { chain_ids, type, value, 2 more }
DnaEntity object { chain_ids, type, value, 2 more }
SequenceRedesignStopResponse object { id, completed_at, created_at, 14 more } A fixed-structure protein sequence redesign run.
A fixed-structure protein sequence redesign run.
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
input: object { entities, num_proteins, structure, 4 more } or object { entities, num_proteins, structure, 4 more } Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
BinderProteinSequenceRedesignRunInputResponse object { entities, num_proteins, structure, 4 more }
entities: array of object { chain_id, role, type } or object { chain_id, role, type, design_motifs } Every chain in the input CIF, assigned exactly once as target or binder.
Every chain in the input CIF, assigned exactly once as target or binder.
BinderSequenceRedesignTargetEntityResponse object { chain_id, role, type } A fixed target chain from the input CIF.
A fixed target chain from the input CIF.
BinderSequenceRedesignBinderEntityResponse object { chain_id, role, type, design_motifs }
design_motifs: optional array of object { filters, residues, type } Residues to redesign. Omit this field to keep the binder chain fixed.
Residues to redesign. Omit this field to keep the binder chain fixed.
filters: array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type } Filters applied to this motif in addition to global_design_filters.
Filters applied to this motif in addition to global_design_filters.
Number of unique filter-passing redesigned proteins to generate.
global_design_filters: optional array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type } Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
GenericProteinSequenceRedesignRunInputResponse object { entities, num_proteins, structure, 4 more }
entities: array of object { chain_id, type, design_motifs } Every chain in the input CIF, assigned exactly once.
Every chain in the input CIF, assigned exactly once.
design_motifs: optional array of object { filters, residues, type } Residues to redesign. Omit this field to keep the chain fixed.
Residues to redesign. Omit this field to keep the chain fixed.
filters: array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type } Filters applied to this motif in addition to global_design_filters.
Filters applied to this motif in addition to global_design_filters.
Number of unique filter-passing redesigned proteins to generate.
global_design_filters: optional array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type } Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
SequenceRedesignResumeResponse object { id, completed_at, created_at, 14 more } A fixed-structure protein sequence redesign run.
A fixed-structure protein sequence redesign run.
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
input: object { entities, num_proteins, structure, 4 more } or object { entities, num_proteins, structure, 4 more } Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
BinderProteinSequenceRedesignRunInputResponse object { entities, num_proteins, structure, 4 more }
entities: array of object { chain_id, role, type } or object { chain_id, role, type, design_motifs } Every chain in the input CIF, assigned exactly once as target or binder.
Every chain in the input CIF, assigned exactly once as target or binder.
BinderSequenceRedesignTargetEntityResponse object { chain_id, role, type } A fixed target chain from the input CIF.
A fixed target chain from the input CIF.
BinderSequenceRedesignBinderEntityResponse object { chain_id, role, type, design_motifs }
design_motifs: optional array of object { filters, residues, type } Residues to redesign. Omit this field to keep the binder chain fixed.
Residues to redesign. Omit this field to keep the binder chain fixed.
filters: array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type } Filters applied to this motif in addition to global_design_filters.
Filters applied to this motif in addition to global_design_filters.
Number of unique filter-passing redesigned proteins to generate.
global_design_filters: optional array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type } Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
GenericProteinSequenceRedesignRunInputResponse object { entities, num_proteins, structure, 4 more }
entities: array of object { chain_id, type, design_motifs } Every chain in the input CIF, assigned exactly once.
Every chain in the input CIF, assigned exactly once.
design_motifs: optional array of object { filters, residues, type } Residues to redesign. Omit this field to keep the chain fixed.
Residues to redesign. Omit this field to keep the chain fixed.
filters: array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type } Filters applied to this motif in addition to global_design_filters.
Filters applied to this motif in addition to global_design_filters.
Number of unique filter-passing redesigned proteins to generate.
global_design_filters: optional array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type } Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
SequenceRedesignEstimateCostResponse object { breakdown, disclaimer, estimated_cost_usd } Estimate response with monetary values encoded as decimal strings to preserve precision.
Estimate response with monetary values encoded as decimal strings to preserve precision.
breakdown: object { application, cost_per_unit_usd, num_units } Cost breakdown for the billed application.
Cost breakdown for the billed application.
application: "structure_and_binding" or "small_molecule_design" or "small_molecule_library_screen" or 4 more
ProteinLibrary Screen
Screen an existing library of proteins against a target structure. Results are scored by binding confidence (likelihood of protein-protein interaction) and structure confidence.
Start a protein library screen
List protein library screens
Get protein library screen status
Get screened protein candidates
Stop a running protein library screen
Resume a stopped protein library screen
Delete protein library screen data
Estimate cost for a protein library screen
ModelsExpand Collapse
LibraryScreenStartResponse object { id, completed_at, created_at, 14 more } A protein library screening pipeline run
A protein library screening pipeline run
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
input: object { proteins, target } Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
target: object { chain_selection, structure, type } or object { entities, type, bonds, 4 more } Target specification (structure template or template-free)
Target specification (structure template or template-free)
StructureTemplateTargetResponse object { chain_selection, structure, type } Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
chain_selection: map[object { chain_type, crop_residues, epitope_residues, 2 more } or object { chain_type } ]Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
StructureTemplateTargetPolymerChainSpec object { chain_type, crop_residues, epitope_residues, 2 more } Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
crop_residues: array of number or "all"0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices where binder contact is desired (the epitope). All indices must be present in crop_residues and must not overlap non_binding_residues.
NoTemplateTargetResponse object { entities, type, bonds, 4 more } Target defined by sequences only, without a 3D structure template
Target defined by sequences only, without a 3D structure template
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 2 moreEntities (proteins, RNA, DNA, ligands) defining the target complex.
Entities (proteins, RNA, DNA, ligands) defining the target complex.
ProteinEntityResponse object { chain_ids, type, value, 2 more }
RnaEntityResponse object { chain_ids, type, value, 2 more }
DnaEntityResponse object { chain_ids, type, value, 2 more }
bonds: optional array of object { atom1, atom2 } Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
constraints: optional array of object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } or object { max_distance_angstrom, token1, token2, 2 more } Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
PocketConstraintResponse object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } Constrains the binder to interact with specific pocket residues on the target.
Constrains the binder to interact with specific pocket residues on the target.
Binding pocket residues keyed by chain ID. Each key is a chain ID (e.g. “A”) and the value is an array of 0-indexed residue indices that define the pocket on that chain.
ContactConstraintResponse object { max_distance_angstrom, token1, token2, 2 more } Maximum-distance contact constraint between two polymer residues or ligand atoms.
Maximum-distance contact constraint between two polymer residues or ligand atoms.
token1: object { chain_id, residue_index, type } or object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandContactTokenResponse object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
token2: object { chain_id, residue_index, type } or object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandContactTokenResponse object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).
progress: object { num_proteins_failed, num_proteins_screened, total_proteins_to_screen, latest_result_id }
LibraryScreenListResponse object { id, completed_at, created_at, 13 more } Summary of a protein library screening pipeline run (excludes input)
Summary of a protein library screening pipeline run (excludes input)
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
progress: object { num_proteins_failed, num_proteins_screened, total_proteins_to_screen, latest_result_id }
LibraryScreenRetrieveResponse object { id, completed_at, created_at, 14 more } A protein library screening pipeline run
A protein library screening pipeline run
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
input: object { proteins, target } Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
target: object { chain_selection, structure, type } or object { entities, type, bonds, 4 more } Target specification (structure template or template-free)
Target specification (structure template or template-free)
StructureTemplateTargetResponse object { chain_selection, structure, type } Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
chain_selection: map[object { chain_type, crop_residues, epitope_residues, 2 more } or object { chain_type } ]Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
StructureTemplateTargetPolymerChainSpec object { chain_type, crop_residues, epitope_residues, 2 more } Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
crop_residues: array of number or "all"0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices where binder contact is desired (the epitope). All indices must be present in crop_residues and must not overlap non_binding_residues.
NoTemplateTargetResponse object { entities, type, bonds, 4 more } Target defined by sequences only, without a 3D structure template
Target defined by sequences only, without a 3D structure template
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 2 moreEntities (proteins, RNA, DNA, ligands) defining the target complex.
Entities (proteins, RNA, DNA, ligands) defining the target complex.
ProteinEntityResponse object { chain_ids, type, value, 2 more }
RnaEntityResponse object { chain_ids, type, value, 2 more }
DnaEntityResponse object { chain_ids, type, value, 2 more }
bonds: optional array of object { atom1, atom2 } Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
constraints: optional array of object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } or object { max_distance_angstrom, token1, token2, 2 more } Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
PocketConstraintResponse object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } Constrains the binder to interact with specific pocket residues on the target.
Constrains the binder to interact with specific pocket residues on the target.
Binding pocket residues keyed by chain ID. Each key is a chain ID (e.g. “A”) and the value is an array of 0-indexed residue indices that define the pocket on that chain.
ContactConstraintResponse object { max_distance_angstrom, token1, token2, 2 more } Maximum-distance contact constraint between two polymer residues or ligand atoms.
Maximum-distance contact constraint between two polymer residues or ligand atoms.
token1: object { chain_id, residue_index, type } or object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandContactTokenResponse object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
token2: object { chain_id, residue_index, type } or object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandContactTokenResponse object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).
progress: object { num_proteins_failed, num_proteins_screened, total_proteins_to_screen, latest_result_id }
LibraryScreenListResultsResponse object { id, artifacts, created_at, 4 more } Result for a single screened protein
Result for a single screened protein
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 2 moreEntities of the screened complex. Includes both screened and fixed entities from the input.
Entities of the screened complex. Includes both screened and fixed entities from the input.
ProteinEntity object { chain_ids, type, value, 2 more }
RnaEntity object { chain_ids, type, value, 2 more }
DnaEntity object { chain_ids, type, value, 2 more }
metrics: object { binding_confidence, helix_fraction, iptm, 4 more } Structural and binding quality metrics for a screened protein
Structural and binding quality metrics for a screened protein
LibraryScreenStopResponse object { id, completed_at, created_at, 14 more } A protein library screening pipeline run
A protein library screening pipeline run
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
input: object { proteins, target } Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
target: object { chain_selection, structure, type } or object { entities, type, bonds, 4 more } Target specification (structure template or template-free)
Target specification (structure template or template-free)
StructureTemplateTargetResponse object { chain_selection, structure, type } Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
chain_selection: map[object { chain_type, crop_residues, epitope_residues, 2 more } or object { chain_type } ]Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
StructureTemplateTargetPolymerChainSpec object { chain_type, crop_residues, epitope_residues, 2 more } Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
crop_residues: array of number or "all"0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices where binder contact is desired (the epitope). All indices must be present in crop_residues and must not overlap non_binding_residues.
NoTemplateTargetResponse object { entities, type, bonds, 4 more } Target defined by sequences only, without a 3D structure template
Target defined by sequences only, without a 3D structure template
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 2 moreEntities (proteins, RNA, DNA, ligands) defining the target complex.
Entities (proteins, RNA, DNA, ligands) defining the target complex.
ProteinEntityResponse object { chain_ids, type, value, 2 more }
RnaEntityResponse object { chain_ids, type, value, 2 more }
DnaEntityResponse object { chain_ids, type, value, 2 more }
bonds: optional array of object { atom1, atom2 } Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
constraints: optional array of object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } or object { max_distance_angstrom, token1, token2, 2 more } Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
PocketConstraintResponse object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } Constrains the binder to interact with specific pocket residues on the target.
Constrains the binder to interact with specific pocket residues on the target.
Binding pocket residues keyed by chain ID. Each key is a chain ID (e.g. “A”) and the value is an array of 0-indexed residue indices that define the pocket on that chain.
ContactConstraintResponse object { max_distance_angstrom, token1, token2, 2 more } Maximum-distance contact constraint between two polymer residues or ligand atoms.
Maximum-distance contact constraint between two polymer residues or ligand atoms.
token1: object { chain_id, residue_index, type } or object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandContactTokenResponse object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
token2: object { chain_id, residue_index, type } or object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandContactTokenResponse object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).
progress: object { num_proteins_failed, num_proteins_screened, total_proteins_to_screen, latest_result_id }
LibraryScreenResumeResponse object { id, completed_at, created_at, 14 more } A protein library screening pipeline run
A protein library screening pipeline run
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
input: object { proteins, target } Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
target: object { chain_selection, structure, type } or object { entities, type, bonds, 4 more } Target specification (structure template or template-free)
Target specification (structure template or template-free)
StructureTemplateTargetResponse object { chain_selection, structure, type } Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
chain_selection: map[object { chain_type, crop_residues, epitope_residues, 2 more } or object { chain_type } ]Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
StructureTemplateTargetPolymerChainSpec object { chain_type, crop_residues, epitope_residues, 2 more } Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
crop_residues: array of number or "all"0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices where binder contact is desired (the epitope). All indices must be present in crop_residues and must not overlap non_binding_residues.
NoTemplateTargetResponse object { entities, type, bonds, 4 more } Target defined by sequences only, without a 3D structure template
Target defined by sequences only, without a 3D structure template
entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 2 moreEntities (proteins, RNA, DNA, ligands) defining the target complex.
Entities (proteins, RNA, DNA, ligands) defining the target complex.
ProteinEntityResponse object { chain_ids, type, value, 2 more }
RnaEntityResponse object { chain_ids, type, value, 2 more }
DnaEntityResponse object { chain_ids, type, value, 2 more }
bonds: optional array of object { atom1, atom2 } Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandAtomResponse object { atom_name, chain_id, type } Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
constraints: optional array of object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } or object { max_distance_angstrom, token1, token2, 2 more } Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
PocketConstraintResponse object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } Constrains the binder to interact with specific pocket residues on the target.
Constrains the binder to interact with specific pocket residues on the target.
Binding pocket residues keyed by chain ID. Each key is a chain ID (e.g. “A”) and the value is an array of 0-indexed residue indices that define the pocket on that chain.
ContactConstraintResponse object { max_distance_angstrom, token1, token2, 2 more } Maximum-distance contact constraint between two polymer residues or ligand atoms.
Maximum-distance contact constraint between two polymer residues or ligand atoms.
token1: object { chain_id, residue_index, type } or object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandContactTokenResponse object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
token2: object { chain_id, residue_index, type } or object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandContactTokenResponse object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).
progress: object { num_proteins_failed, num_proteins_screened, total_proteins_to_screen, latest_result_id }
LibraryScreenEstimateCostResponse object { breakdown, disclaimer, estimated_cost_usd } Estimate response with monetary values encoded as decimal strings to preserve precision.
Estimate response with monetary values encoded as decimal strings to preserve precision.
breakdown: object { application, cost_per_unit_usd, num_units } Cost breakdown for the billed application.
Cost breakdown for the billed application.