Start a protein de novo design run
Create a new design run that generates novel protein binder candidates
ParametersExpand Collapse
body ProteinDesignStartParams
BinderSpecification param.Field[ProteinDesignStartParamsBinderSpecificationUnion]Binder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, or boltz_curated for Boltz-managed nanobody and antibody defaults.
Binder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, or boltz_curated for Boltz-managed nanobody and antibody defaults.
type ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpec struct{…}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.
ChainSelection map[string, ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionUnion]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.
type ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpec struct{…}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.
CropResidues ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecCropResiduesUnion0-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.
DesignMotifs []ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecDesignMotifUnionOptionalOptional 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.
type ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecDesignMotifReplacementMotif struct{…}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.
type ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecDesignMotifInsertionMotif struct{…}Insert a designed segment at a specific position in the sequence.
Insert a designed segment at a specific position in the sequence.
0-indexed position after which to insert. Use -1 to insert before the first residue.
Modality ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecModality
Structure ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecStructureUnionHow 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 ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecRulesOptionalConstraints 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)
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpec struct{…}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 []ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityUnionBinder 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.
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityDesignedProteinEntity struct{…}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.
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityFixedProteinEntity struct{…}A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityFixedRnaEntity struct{…}
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityFixedDnaEntity struct{…}
Modality ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecModality
Bonds []ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecBondOptionalCovalent 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 ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecBondAtom1UnionLigand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Atom2 ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecBondAtom2UnionLigand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Rules ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecRulesOptionalConstraints 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)
type ProteinDesignStartParamsBinderSpecificationBoltzCuratedBinderSpec struct{…}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 ProteinDesignStartParamsBinderSpecificationBoltzCuratedBinderSpecBinderBoltz-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 ProteinDesignStartParamsBinderSpecificationBoltzCuratedBinderSpecRulesOptionalConstraints 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 param.Field[ProteinDesignStartParamsTargetUnion]Target specification (structure template or template-free)
Target specification (structure template or template-free)
type ProteinDesignStartParamsTargetStructureTemplateTarget struct{…}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.
ChainSelection map[string, ProteinDesignStartParamsTargetStructureTemplateTargetChainSelectionUnion]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.
type ProteinDesignStartParamsTargetStructureTemplateTargetChainSelectionStructureTemplateTargetPolymerChainSpec struct{…}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.
CropResidues ProteinDesignStartParamsTargetStructureTemplateTargetChainSelectionStructureTemplateTargetPolymerChainSpecCropResiduesUnion0-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.
type ProteinDesignStartParamsTargetNoTemplateTarget struct{…}Target defined by sequences only, without a 3D structure template
Target defined by sequences only, without a 3D structure template
Entities []ProteinDesignStartParamsTargetNoTemplateTargetEntityUnionEntities (proteins, RNA, DNA, ligands) defining the target complex.
Entities (proteins, RNA, DNA, ligands) defining the target complex.
type ProteinDesignStartParamsTargetNoTemplateTargetEntityProteinEntity struct{…}
type ProteinDesignStartParamsTargetNoTemplateTargetEntityRnaEntity struct{…}
type ProteinDesignStartParamsTargetNoTemplateTargetEntityDnaEntity struct{…}
Bonds []ProteinDesignStartParamsTargetNoTemplateTargetBondOptionalCovalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
Atom1 ProteinDesignStartParamsTargetNoTemplateTargetBondAtom1UnionLigand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Atom2 ProteinDesignStartParamsTargetNoTemplateTargetBondAtom2UnionLigand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Constraints []ProteinDesignStartParamsTargetNoTemplateTargetConstraintUnionOptionalStructural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
type ProteinDesignStartParamsTargetNoTemplateTargetConstraintPocketConstraint struct{…}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.
type ProteinDesignStartParamsTargetNoTemplateTargetConstraintContactConstraint struct{…}Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Token1 ProteinDesignStartParamsTargetNoTemplateTargetConstraintContactConstraintToken1UnionLigand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
type ProteinDesignStartParamsTargetNoTemplateTargetConstraintContactConstraintToken1PolymerContactToken struct{…}
Token2 ProteinDesignStartParamsTargetNoTemplateTargetConstraintContactConstraintToken2UnionLigand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
type ProteinDesignStartParamsTargetNoTemplateTargetConstraintContactConstraintToken2PolymerContactToken struct{…}
Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).
ReturnsExpand Collapse
type ProteinDesignStartResponse struct{…}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 ProteinDesignStartResponseInputPipeline input (null if data deleted)
Pipeline input (null if data deleted)
BinderSpecification ProteinDesignStartResponseInputBinderSpecificationUnionBinder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, or boltz_curated for Boltz-managed nanobody and antibody defaults.
Binder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, or boltz_curated for Boltz-managed nanobody and antibody defaults.
type ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponse struct{…}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.
ChainSelection map[string, ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionUnion]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.
type ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpec struct{…}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.
CropResidues ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecCropResiduesUnion0-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.
DesignMotifs []ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifUnionOptionalOptional 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.
type ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifReplacementMotif struct{…}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.
type ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifInsertionMotif struct{…}Insert a designed segment at a specific position in the sequence.
Insert a designed segment at a specific position in the sequence.
0-indexed position after which to insert. Use -1 to insert before the first residue.
Modality ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponseModality
Structure ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponseStructure
Rules ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponseRulesOptionalConstraints 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)
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponse struct{…}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 []ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityUnionBinder 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.
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityDesignedProteinEntityResponse struct{…}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.
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedProteinEntityResponse struct{…}A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedRnaEntityResponse struct{…}
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedDnaEntityResponse struct{…}
Modality ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseModality
Bonds []ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseBondOptionalCovalent 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 ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseBondAtom1UnionLigand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Atom2 ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseBondAtom2UnionLigand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Rules ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseRulesOptionalConstraints 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)
type ProteinDesignStartResponseInputBinderSpecificationBoltzCuratedBinderSpecResponse struct{…}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 ProteinDesignStartResponseInputBinderSpecificationBoltzCuratedBinderSpecResponseBinderBoltz-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 ProteinDesignStartResponseInputBinderSpecificationBoltzCuratedBinderSpecResponseRulesOptionalConstraints 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 ProteinDesignStartResponseInputTargetUnionTarget specification (structure template or template-free)
Target specification (structure template or template-free)
type ProteinDesignStartResponseInputTargetStructureTemplateTargetResponse struct{…}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.
ChainSelection map[string, ProteinDesignStartResponseInputTargetStructureTemplateTargetResponseChainSelectionUnion]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.
type ProteinDesignStartResponseInputTargetStructureTemplateTargetResponseChainSelectionStructureTemplateTargetPolymerChainSpec struct{…}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.
CropResidues ProteinDesignStartResponseInputTargetStructureTemplateTargetResponseChainSelectionStructureTemplateTargetPolymerChainSpecCropResiduesUnion0-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.
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponse struct{…}Target defined by sequences only, without a 3D structure template
Target defined by sequences only, without a 3D structure template
Entities []ProteinDesignStartResponseInputTargetNoTemplateTargetResponseEntityUnionEntities (proteins, RNA, DNA, ligands) defining the target complex.
Entities (proteins, RNA, DNA, ligands) defining the target complex.
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseEntityProteinEntityResponse struct{…}
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseEntityRnaEntityResponse struct{…}
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseEntityDnaEntityResponse struct{…}
Bonds []ProteinDesignStartResponseInputTargetNoTemplateTargetResponseBondOptionalCovalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
Atom1 ProteinDesignStartResponseInputTargetNoTemplateTargetResponseBondAtom1UnionLigand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Atom2 ProteinDesignStartResponseInputTargetNoTemplateTargetResponseBondAtom2UnionLigand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Constraints []ProteinDesignStartResponseInputTargetNoTemplateTargetResponseConstraintUnionOptionalStructural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseConstraintPocketConstraintResponse struct{…}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.
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseConstraintContactConstraintResponse struct{…}Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Token1 ProteinDesignStartResponseInputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1UnionLigand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1PolymerContactTokenResponse struct{…}
Token2 ProteinDesignStartResponseInputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2UnionLigand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2PolymerContactTokenResponse struct{…}
Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).
Start a protein de novo design run
package main
import (
"context"
"fmt"
"github.com/boltz-bio/boltz-api-go"
"github.com/boltz-bio/boltz-api-go/option"
)
func main() {
client := boltzapi.NewClient(
option.WithAPIKey("My API Key"),
)
response, err := client.Protein.Design.Start(context.TODO(), boltzapi.ProteinDesignStartParams{
BinderSpecification: boltzapi.ProteinDesignStartParamsBinderSpecificationUnion{
OfProteinDesignStartsBinderSpecificationStructureTemplateBinderSpec: &boltzapi.ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpec{
ChainSelection: map[string]boltzapi.ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionUnion{
"B": boltzapi.ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionUnion{
OfProteinDesignStartsBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpec: &boltzapi.ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpec{
CropResidues: boltzapi.ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecCropResiduesUnion{
OfIntArray: []int64{0, 1, 2, 3, 4, 5, 6, 7, 8, 9},
},
},
},
},
Modality: boltzapi.ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecModalityPeptide,
Structure: boltzapi.ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecStructureUnion{
OfProteinDesignStartsBinderSpecificationStructureTemplateBinderSpecStructureURLSource: &boltzapi.ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecStructureURLSource{
URL: "https://example.com",
},
},
},
},
NumProteins: 10,
Target: boltzapi.ProteinDesignStartParamsTargetUnion{
OfProteinDesignStartsTargetStructureTemplateTarget: &boltzapi.ProteinDesignStartParamsTargetStructureTemplateTarget{
ChainSelection: map[string]boltzapi.ProteinDesignStartParamsTargetStructureTemplateTargetChainSelectionUnion{
"A": boltzapi.ProteinDesignStartParamsTargetStructureTemplateTargetChainSelectionUnion{
OfProteinDesignStartsTargetStructureTemplateTargetChainSelectionStructureTemplateTargetPolymerChainSpec: &boltzapi.ProteinDesignStartParamsTargetStructureTemplateTargetChainSelectionStructureTemplateTargetPolymerChainSpec{
CropResidues: boltzapi.ProteinDesignStartParamsTargetStructureTemplateTargetChainSelectionStructureTemplateTargetPolymerChainSpecCropResiduesUnion{
OfIntArray: []int64{0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12},
},
},
},
},
Structure: boltzapi.ProteinDesignStartParamsTargetStructureTemplateTargetStructureUnion{
OfProteinDesignStartsTargetStructureTemplateTargetStructureURLSource: &boltzapi.ProteinDesignStartParamsTargetStructureTemplateTargetStructureURLSource{
URL: "https://example.com",
},
},
},
},
})
if err != nil {
panic(err.Error())
}
fmt.Printf("%+v\n", response.ID)
}
{
"id": "id",
"completed_at": "2019-12-27T18:11:19.117Z",
"created_at": "2019-12-27T18:11:19.117Z",
"data_deleted_at": "2019-12-27T18:11:19.117Z",
"engine": "boltzprot",
"engine_version": "1.0",
"error": {
"code": "code",
"message": "message",
"details": {}
},
"input": {
"binder_specification": {
"chain_selection": {
"B": {
"chain_type": "polymer",
"crop_residues": [
0,
1,
2,
3,
4,
5,
6,
7,
8,
9
],
"design_motifs": [
{
"design_length_range": {
"max": 8,
"min": 4
},
"end_index": 5,
"start_index": 0,
"type": "replacement"
}
]
}
},
"modality": "peptide",
"structure": {
"url": "https://example.com",
"url_expires_at": "2019-12-27T18:11:19.117Z"
},
"type": "structure_template",
"rules": {
"excluded_amino_acids": [
"x"
],
"excluded_sequence_motifs": [
"string"
],
"max_hydrophobic_fraction": 0
}
},
"num_proteins": 10,
"target": {
"chain_selection": {
"A": {
"chain_type": "polymer",
"crop_residues": [
0,
1,
2,
3,
4,
5,
6,
7,
8,
9,
10,
11,
12
],
"epitope_residues": [
10,
11,
12
],
"flexible_residues": [
5,
6,
7
],
"non_binding_residues": [
0,
1,
2
]
}
},
"structure": {
"url": "https://example.com",
"url_expires_at": "2019-12-27T18:11:19.117Z"
},
"type": "structure_template"
},
"idempotency_key": "idempotency_key",
"workspace_id": "workspace_id"
},
"livemode": true,
"pipeline": "boltzprot",
"pipeline_version": "1.0",
"progress": {
"num_proteins_generated": 0,
"total_proteins_to_generate": 1,
"latest_result_id": "latest_result_id"
},
"started_at": "2019-12-27T18:11:19.117Z",
"status": "pending",
"stopped_at": "2019-12-27T18:11:19.117Z",
"workspace_id": "workspace_id",
"idempotency_key": "idempotency_key"
}Returns Examples
{
"id": "id",
"completed_at": "2019-12-27T18:11:19.117Z",
"created_at": "2019-12-27T18:11:19.117Z",
"data_deleted_at": "2019-12-27T18:11:19.117Z",
"engine": "boltzprot",
"engine_version": "1.0",
"error": {
"code": "code",
"message": "message",
"details": {}
},
"input": {
"binder_specification": {
"chain_selection": {
"B": {
"chain_type": "polymer",
"crop_residues": [
0,
1,
2,
3,
4,
5,
6,
7,
8,
9
],
"design_motifs": [
{
"design_length_range": {
"max": 8,
"min": 4
},
"end_index": 5,
"start_index": 0,
"type": "replacement"
}
]
}
},
"modality": "peptide",
"structure": {
"url": "https://example.com",
"url_expires_at": "2019-12-27T18:11:19.117Z"
},
"type": "structure_template",
"rules": {
"excluded_amino_acids": [
"x"
],
"excluded_sequence_motifs": [
"string"
],
"max_hydrophobic_fraction": 0
}
},
"num_proteins": 10,
"target": {
"chain_selection": {
"A": {
"chain_type": "polymer",
"crop_residues": [
0,
1,
2,
3,
4,
5,
6,
7,
8,
9,
10,
11,
12
],
"epitope_residues": [
10,
11,
12
],
"flexible_residues": [
5,
6,
7
],
"non_binding_residues": [
0,
1,
2
]
}
},
"structure": {
"url": "https://example.com",
"url_expires_at": "2019-12-27T18:11:19.117Z"
},
"type": "structure_template"
},
"idempotency_key": "idempotency_key",
"workspace_id": "workspace_id"
},
"livemode": true,
"pipeline": "boltzprot",
"pipeline_version": "1.0",
"progress": {
"num_proteins_generated": 0,
"total_proteins_to_generate": 1,
"latest_result_id": "latest_result_id"
},
"started_at": "2019-12-27T18:11:19.117Z",
"status": "pending",
"stopped_at": "2019-12-27T18:11:19.117Z",
"workspace_id": "workspace_id",
"idempotency_key": "idempotency_key"
}