## Start `$ boltz-api protein:library-screen start` **post** `/compute/v1/protein/library-screen` Screen a set of protein candidates against a target ### Parameters - `--protein: array of object { entities, id }` List of protein entries to screen. - `--target: object { chain_selection, structure, type } or object { entities, type, bonds, 3 more }` Target specification (structure template or template-free) - `--idempotency-key: optional string` Client-provided key to prevent duplicate submissions on retries - `--workspace-id: optional string` Target workspace ID (admin keys only; ignored for workspace keys) ### Returns - `ProteinLibraryScreenStartResponse: object { id, completed_at, created_at, 12 more }` A protein library screening engine run - `id: string` Unique ProteinLibraryScreen identifier - `completed_at: string` - `created_at: string` - `data_deleted_at: string` When the input, output, and result data was permanently deleted. Null if data has not been deleted. - `engine: "boltz-protein-screen"` Engine used for protein library screen - `"boltz-protein-screen"` - `engine_version: string` Engine version used for protein library screen - `error: object { code, message, details }` - `code: string` Machine-readable error code - `message: string` Human-readable error message - `details: optional unknown` Additional field-level error details keyed by input path, when available. - `input: object { proteins, target }` Pipeline input (null if data deleted) - `proteins: object { url, url_expires_at }` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `target: object { chain_selection, structure, type } or object { entities, type, bonds, 3 more }` 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. - `chain_selection: map[object { chain_type, crop_residues, epitope_residues, flexible_residues } or object { chain_type } ]` Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the engine run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, and which are flexible. - `StructureTemplateTargetPolymerChainSpec: object { chain_type, crop_residues, epitope_residues, flexible_residues }` Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target. - `chain_type: "polymer"` - `"polymer"` - `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 engine run. - `union_member_0: array of number` 0-indexed residue indices to keep - `union_member_1: "all"` - `"all"` - `epitope_residues: optional array of number` 0-indexed residue indices where binder contact is desired (the epitope). All indices must be present in crop_residues. - `flexible_residues: optional array of number` 0-indexed residue indices allowed to move during design (e.g. flexible loop regions). All indices must be present in crop_residues. - `StructureTemplateTargetLigandChainSpec: object { chain_type }` Per-chain specification for a ligand chain in a structure template target. The full ligand is always included. - `chain_type: "ligand"` - `"ligand"` - `structure: object { url, url_expires_at }` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `type: "structure_template"` - `"structure_template"` - `NoTemplateTargetResponse: object { entities, type, bonds, 3 more }` 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 more` Entities (proteins, RNA, DNA, ligands) defining the target complex. - `ProteinEntityResponse: object { chain_ids, type, value, 2 more }` - `chain_ids: array of string` Chain IDs for this entity - `type: "protein"` - `"protein"` - `value: string` Amino acid sequence (one-letter codes) - `cyclic: optional boolean` Whether the sequence is cyclic - `modifications: optional array of object { residue_index, type, value } or object { residue_index, type, value }` Post-translational modifications. Optional; defaults to an empty list when omitted. - `CCDModificationResponse: object { residue_index, type, value }` - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` - `"ccd"` - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `SmilesModificationResponse: object { residue_index, type, value }` - `residue_index: number` 0-based index of the residue to modify - `type: "smiles"` - `"smiles"` - `value: string` SMILES string for the modification - `RNAEntityResponse: object { chain_ids, type, value, 2 more }` - `chain_ids: array of string` Chain IDs for this entity - `type: "rna"` - `"rna"` - `value: string` RNA nucleotide sequence (A, C, G, U, N) - `cyclic: optional boolean` Whether the sequence is cyclic - `modifications: optional array of object { residue_index, type, value } or object { residue_index, type, value }` Chemical modifications. Optional; defaults to an empty list when omitted. - `CCDModificationResponse: object { residue_index, type, value }` - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` - `"ccd"` - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `SmilesModificationResponse: object { residue_index, type, value }` - `residue_index: number` 0-based index of the residue to modify - `type: "smiles"` - `"smiles"` - `value: string` SMILES string for the modification - `DNAEntityResponse: object { chain_ids, type, value, 2 more }` - `chain_ids: array of string` Chain IDs for this entity - `type: "dna"` - `"dna"` - `value: string` DNA nucleotide sequence (A, C, G, T, N) - `cyclic: optional boolean` Whether the sequence is cyclic - `modifications: optional array of object { residue_index, type, value } or object { residue_index, type, value }` Chemical modifications. Optional; defaults to an empty list when omitted. - `CCDModificationResponse: object { residue_index, type, value }` - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` - `"ccd"` - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `SmilesModificationResponse: object { residue_index, type, value }` - `residue_index: number` 0-based index of the residue to modify - `type: "smiles"` - `"smiles"` - `value: string` SMILES string for the modification - `LigandCCDEntityResponse: object { chain_ids, type, value }` - `chain_ids: array of string` Chain IDs for this ligand - `type: "ligand_ccd"` - `"ligand_ccd"` - `value: string` CCD code (e.g., ATP, ADP) - `LigandSmilesEntityResponse: object { chain_ids, type, value }` - `chain_ids: array of string` Chain IDs for this ligand - `type: "ligand_smiles"` - `"ligand_smiles"` - `value: string` SMILES string representing the ligand - `type: "no_template"` - `"no_template"` - `bonds: optional array of object { atom1, atom2 }` Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtomResponse: object { atom_name, chain_id, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtomResponse: object { atom_name, chain_id, residue_index, type }` - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB) - `chain_id: string` Chain ID containing the atom - `residue_index: number` 0-based residue index - `type: "polymer_atom"` - `"polymer_atom"` - `atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtomResponse: object { atom_name, chain_id, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtomResponse: object { atom_name, chain_id, residue_index, type }` - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB) - `chain_id: string` Chain ID containing the atom - `residue_index: number` 0-based residue index - `type: "polymer_atom"` - `"polymer_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). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `PocketConstraintResponse: object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more }` Constrains the binder to interact with specific pocket residues on the target. - `binder_chain_id: string` Chain ID of the binder molecule - `contact_residues: map[array of number]` 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. - `max_distance_angstrom: number` Maximum allowed distance in Angstroms between binder and pocket residues. Typical range: 4-8 A. - `type: "pocket"` - `"pocket"` - `force: optional boolean` Whether to force the constraint - `ContactConstraintResponse: object { max_distance_angstrom, token1, token2, 2 more }` Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `max_distance_angstrom: number` Maximum distance in Angstroms - `token1: object { chain_id, residue_index, type } or object { atom_name, chain_id, type }` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactTokenResponse: object { chain_id, residue_index, type }` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactTokenResponse: object { atom_name, chain_id, type }` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `token2: object { chain_id, residue_index, type } or object { atom_name, chain_id, type }` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactTokenResponse: object { chain_id, residue_index, type }` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactTokenResponse: object { atom_name, chain_id, type }` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `type: "contact"` - `"contact"` - `force: optional boolean` Whether to force the constraint - `epitope_ligand_chains: optional array of string` Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection). - `epitope_residues: optional map[array of number]` Polymer chain residues where binder contact is desired (the epitope). Each key is a chain ID of a polymer entity, each value is an array of 0-indexed residue indices. - `livemode: boolean` Whether this resource was created with a live API key. - `progress: object { num_proteins_failed, num_proteins_screened, total_proteins_to_screen, latest_result_id }` - `num_proteins_failed: number` Number of accepted proteins that reached terminal failure during screening. - `num_proteins_screened: number` Number of accepted proteins that produced usable screening results. - `total_proteins_to_screen: number` Total number of proteins accepted into the screening run. - `latest_result_id: optional string` ID of the latest result - `started_at: string` - `status: "pending" or "running" or "succeeded" or 2 more` - `"pending"` - `"running"` - `"succeeded"` - `"failed"` - `"stopped"` - `stopped_at: string` - `workspace_id: string` Workspace ID - `idempotency_key: optional string` Client-provided idempotency key ### Example ```cli boltz-api protein:library-screen start \ --protein '{entities: [{chain_ids: [string], type: protein, value: value, cyclic: true, modifications: [{residue_index: 0, type: ccd, value: value}]}], id: id}' \ --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]}}, structure: {type: url, url: https://example.com}, type: structure_template}' ```