Share Links
Share read-only access to predictions and pipeline runs by issuing time-limited links that visitors can open without an API key or, for email-restricted links, after signing in with an allowed email. A share link is scoped to a single workspace and bundles one or more predictions and pipeline runs. The link ID is itself the bearer credential; treat it as a secret. Create, retrieve, and archive require an API key or supported OAuth bearer token with read permission on every referenced resource. Retrieving metadata remains available after expiry or archive. Viewing content and listing shared pipeline results are gated by the link ID and the link’s access mode. Archiving a link revokes public access immediately; subsequent content reads return 404. The underlying predictions and pipelines are unaffected and remain accessible through their own authenticated endpoints.
Create a share link
Retrieve a share link
Archive a share link
Read a share link
List pipeline results from a share link
ModelsExpand Collapse
ShareLinkCreateResponse object { id, access_parameters, archived_at, 6 more }
Share link ID. This value is the bearer credential used to access the linked resources — treat it as a secret.
access_parameters: object { access_mode } or object { access_mode, allowed_emails } Access-control parameters for the share link. Discriminated by access_mode: public requires no other fields; email requires a non-empty allowed_emails list.
Access-control parameters for the share link. Discriminated by access_mode: public requires no other fields; email requires a non-empty allowed_emails list.
ShareLinkRetrieveResponse object { id, access_parameters, archived_at, 6 more }
Share link ID. This value is the bearer credential used to access the linked resources — treat it as a secret.
access_parameters: object { access_mode } or object { access_mode, allowed_emails } Access-control parameters for the share link. Discriminated by access_mode: public requires no other fields; email requires a non-empty allowed_emails list.
Access-control parameters for the share link. Discriminated by access_mode: public requires no other fields; email requires a non-empty allowed_emails list.
ShareLinkReadResponse object { id, created_at, expires_at, 3 more }
pipelines: array of object { id, completed_at, created_at, 14 more } or object { id, completed_at, created_at, 14 more } or object { id, completed_at, created_at, 14 more } or 4 morePipelines exposed by this share link, in the order they were registered.
Pipelines exposed by this share link, in the order they were registered.
ProteinDesignRunResponse object { id, completed_at, created_at, 14 more } A protein design run.
A protein design 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 { binder_specification, num_proteins, target, 2 more } or object { binder, num_proteins, target, 5 more } or object { entities, num_proteins, templates, 5 more } Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
ProteinDesignRunInputResponse object { binder_specification, num_proteins, target, 2 more } Deprecated legacy protein binder design input. Use BinderProteinDesignRunInput for binder design or GenericProteinDesignRunInput for generic protein design. Legacy inputs remain accepted during migration.
Deprecated legacy protein binder design input. Use BinderProteinDesignRunInput for binder design or GenericProteinDesignRunInput for generic protein design. Legacy inputs remain accepted during migration.
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 4 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 }
GlycanEntityResponse object { bonds, chain_ids, residues, type } Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
bonds: array of object { atom1, atom2 } Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
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, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
atom2: object { atom_name, chain_id, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use 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 4 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 }
GlycanEntityResponse object { bonds, chain_ids, residues, type } Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
bonds: array of object { atom1, atom2 } Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
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, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
atom2: object { atom_name, chain_id, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use 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 3 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 }
GlycanEntityResponse object { bonds, chain_ids, residues, type } Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
bonds: array of object { atom1, atom2 } Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
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, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
atom2: object { atom_name, chain_id, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use 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).
BinderProteinDesignRunInputResponse object { binder, num_proteins, target, 5 more }
binder: object { entities, modality, bonds } or object { binder, type } or object { specifications, type }
SingleProteinDesignBinderResponse object { entities, modality, bonds }
entities: array of object { chain_id, crop_residues, template_id, 2 more } or object { entity, type }
ProteinDesignFromTemplateEntityResponse object { chain_id, crop_residues, template_id, 2 more }
design_motifs: optional array of object { design_length_range, end_index, filters, 2 more } or object { after_residue_index, design_length_range, filters, type } Regions to design. Omit this field to keep the selected chain fixed.
Regions to design. Omit this field to keep the selected chain fixed.
ProteinDesignReplacementMotifResponse object { design_length_range, end_index, filters, 2 more }
0-indexed last replaced residue within the cropped chain selection, inclusive.
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.
ProteinDesignInsertionMotifResponse object { after_residue_index, design_length_range, filters, type }
0-indexed residue within the cropped chain selection after which to insert; -1 inserts before the first selected residue.
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.
ProteinDesignNoTemplateEntityResponse object { entity, type } A template-free entity. The nested entity retains the existing protein-design entity contract, including the compact designed_protein value syntax.
A template-free entity. The nested entity retains the existing protein-design entity contract, including the compact designed_protein value syntax.
entity: object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 4 moreProtein binder entity with designed and/or fixed segments.
Protein binder entity with designed and/or fixed segments.
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 }
GlycanEntityResponse object { bonds, chain_ids, residues, type } Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
bonds: array of object { atom1, atom2 } Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
bonds: optional array of object { atom1, atom2 }
atom1: object { atom_name, chain_id, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
atom2: object { atom_name, chain_id, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
UniformlySampledProteinDesignBinderResponse object { specifications, type }
specifications: array of object { entities, modality, bonds } or object { binder, type }
SingleProteinDesignBinderResponse object { entities, modality, bonds }
entities: array of object { chain_id, crop_residues, template_id, 2 more } or object { entity, type }
ProteinDesignFromTemplateEntityResponse object { chain_id, crop_residues, template_id, 2 more }
design_motifs: optional array of object { design_length_range, end_index, filters, 2 more } or object { after_residue_index, design_length_range, filters, type } Regions to design. Omit this field to keep the selected chain fixed.
Regions to design. Omit this field to keep the selected chain fixed.
ProteinDesignReplacementMotifResponse object { design_length_range, end_index, filters, 2 more }
0-indexed last replaced residue within the cropped chain selection, inclusive.
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.
ProteinDesignInsertionMotifResponse object { after_residue_index, design_length_range, filters, type }
0-indexed residue within the cropped chain selection after which to insert; -1 inserts before the first selected residue.
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.
ProteinDesignNoTemplateEntityResponse object { entity, type } A template-free entity. The nested entity retains the existing protein-design entity contract, including the compact designed_protein value syntax.
A template-free entity. The nested entity retains the existing protein-design entity contract, including the compact designed_protein value syntax.
entity: object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 4 moreProtein binder entity with designed and/or fixed segments.
Protein binder entity with designed and/or fixed segments.
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 }
GlycanEntityResponse object { bonds, chain_ids, residues, type } Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
bonds: array of object { atom1, atom2 } Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
bonds: optional array of object { atom1, atom2 }
atom1: object { atom_name, chain_id, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
atom2: object { atom_name, chain_id, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Number of protein designs to generate. Must be between 10 and 1,000,000.
target: object { entities, bonds } Fixed target entities. Binding annotations are entity-local so repeated chain IDs across templates remain unambiguous.
Fixed target entities. Binding annotations are entity-local so repeated chain IDs across templates remain unambiguous.
entities: array of object { chain_id, crop_residues, template_id, 4 more } or object { entity, type, epitope_residues, 2 more }
ProteinDesignTargetFromTemplateEntityResponse object { chain_id, crop_residues, template_id, 4 more } A fixed target chain selected from a template. Target entities cannot contain design_motifs.
A fixed target chain selected from a template. Target entities cannot contain design_motifs.
ProteinDesignTargetNoTemplateEntityResponse object { entity, type, epitope_residues, 2 more }
entity: 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 moreBranched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
ProteinEntityResponse object { chain_ids, type, value, 2 more }
RnaEntityResponse object { chain_ids, type, value, 2 more }
DnaEntityResponse object { chain_ids, type, value, 2 more }
GlycanEntityResponse object { bonds, chain_ids, residues, type } Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
bonds: array of object { atom1, atom2 } Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
bonds: optional array of object { atom1, atom2 }
atom1: object { atom_name, chain_id, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
atom2: object { atom_name, chain_id, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
templates: array of object { id, url, url_expires_at } or object { id, url, url_expires_at }
global_design_filters: optional array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type } Filters applied to every designed region. When omitted, cysteine is excluded. Pass [] to disable global filters.
Filters applied to every designed region. When omitted, cysteine is excluded. Pass [] to disable global filters.
GenericProteinDesignRunInputResponse object { entities, num_proteins, templates, 5 more }
entities: array of object { chain_id, crop_residues, template_id, 2 more } or object { entity, type } or object { output_chain_id, segments, type }
ProteinDesignFromTemplateEntityResponse object { chain_id, crop_residues, template_id, 2 more }
design_motifs: optional array of object { design_length_range, end_index, filters, 2 more } or object { after_residue_index, design_length_range, filters, type } Regions to design. Omit this field to keep the selected chain fixed.
Regions to design. Omit this field to keep the selected chain fixed.
ProteinDesignReplacementMotifResponse object { design_length_range, end_index, filters, 2 more }
0-indexed last replaced residue within the cropped chain selection, inclusive.
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.
ProteinDesignInsertionMotifResponse object { after_residue_index, design_length_range, filters, type }
0-indexed residue within the cropped chain selection after which to insert; -1 inserts before the first selected residue.
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.
ProteinDesignNoTemplateEntityResponse object { entity, type } A template-free entity. The nested entity retains the existing protein-design entity contract, including the compact designed_protein value syntax.
A template-free entity. The nested entity retains the existing protein-design entity contract, including the compact designed_protein value syntax.
entity: object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 4 moreProtein binder entity with designed and/or fixed segments.
Protein binder entity with designed and/or fixed segments.
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 }
GlycanEntityResponse object { bonds, chain_ids, residues, type } Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
bonds: array of object { atom1, atom2 } Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
FusionProteinEntityResponse object { output_chain_id, segments, type } An ordered fusion protein whose segments are concatenated into one surviving output chain.
An ordered fusion protein whose segments are concatenated into one surviving output chain.
segments: array of object { chain_id, crop_residues, template_id, 2 more } or object { entity, type }
ProteinDesignFromTemplateEntityResponse object { chain_id, crop_residues, template_id, 2 more }
design_motifs: optional array of object { design_length_range, end_index, filters, 2 more } or object { after_residue_index, design_length_range, filters, type } Regions to design. Omit this field to keep the selected chain fixed.
Regions to design. Omit this field to keep the selected chain fixed.
ProteinDesignReplacementMotifResponse object { design_length_range, end_index, filters, 2 more }
0-indexed last replaced residue within the cropped chain selection, inclusive.
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.
ProteinDesignInsertionMotifResponse object { after_residue_index, design_length_range, filters, type }
0-indexed residue within the cropped chain selection after which to insert; -1 inserts before the first selected residue.
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.
FusionProteinNoTemplateSegmentResponse object { entity, type }
entity: object { type, value, cyclic, modifications } or object { type, value, cyclic, modifications }
FusionProteinFixedSegmentResponse object { type, value, cyclic, modifications }
FusionProteinDesignedSegmentResponse object { type, value, cyclic, modifications }
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.
Number of protein designs to generate. Must be between 10 and 1,000,000.
templates: array of object { id, url, url_expires_at } or object { id, url, url_expires_at }
bonds: optional array of object { atom1, atom2 }
atom1: object { atom_name, chain_id, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
atom2: object { atom_name, chain_id, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
global_design_filters: optional array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type } Filters applied to every designed region. When omitted, cysteine is excluded. Pass [] to disable global filters.
Filters applied to every designed region. When omitted, cysteine is excluded. Pass [] to disable global filters.
ProteinRedesignRun object { id, completed_at, created_at, 14 more } A fixed-structure binder sequence redesign run
A fixed-structure binder 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 { chains_config, num_proteins, structure, 3 more } Input for protein redesign from a complete target/binder CIF complex.
Input for protein redesign from a complete target/binder CIF complex.
chains_config: object { binder_chains, target_chains } Complete chain assignment for the input CIF. Every CIF chain must appear exactly once, either under target_chains or binder_chains.
Complete chain assignment for the input CIF. Every CIF chain must appear exactly once, either under target_chains or binder_chains.
binder_chains: map[object { chain_type, designed_residues } or object { chain_type } ]Binder chains keyed by CIF chain ID. Protein binder chains may provide designed_residues; at least 5 total unique designed residues are required across all protein binder chains. Target and binder chains must be disjoint and together cover every chain in the CIF.
Binder chains keyed by CIF chain ID. Protein binder chains may provide designed_residues; at least 5 total unique designed residues are required across all protein binder chains. Target and binder chains must be disjoint and together cover every chain in the CIF.
Number of unique filter-passing redesigned proteins to generate.
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)
ProteinSequenceRedesignRun 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.
ProteinLibraryScreen 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 3 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 }
GlycanEntityResponse object { bonds, chain_ids, residues, type } Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
bonds: array of object { atom1, atom2 } Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
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, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
atom2: object { atom_name, chain_id, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use 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 }
SmDesignRun object { id, completed_at, created_at, 14 more } A small molecule design pipeline run that generates novel molecules
A small molecule design pipeline run that generates novel molecules
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
input: object { num_molecules, target, chemical_space, 3 more } Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
Number of molecules to generate. Must be between 10 and 1,000,000.
target: object { entities, bonds, constraints, 3 more } Target protein sequences for small molecule design or screening.
Target protein sequences for small molecule design or screening.
entities: array of object { chain_ids, type, value, 2 more } or object { bonds, chain_ids, residues, type } Protein and glycan entities defining the target structure. At least one protein entity is required.
Protein and glycan entities defining the target structure. At least one protein entity is required.
ProteinEntityResponse object { chain_ids, type, value, 2 more }
GlycanEntityResponse object { bonds, chain_ids, residues, type } Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
bonds: array of object { atom1, atom2 } Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
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, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
atom2: object { atom_name, chain_id, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use 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.
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 binding pocket on that chain. When provided, these residues guide pocket extraction and add a derived pocket constraint during affinity predictions. That derived constraint remains separate from any explicit pocket constraints in target.constraints. When omitted, the model auto-detects the pocket.
chemical_space: optional "enamine_real" or "none" or "wuxi_galaxi"Chemical space to constrain generated molecules. Use ‘enamine_real’ for the Enamine REAL chemical space, ‘wuxi_galaxi’ for the WuXi GalaXi chemical space, or ‘none’ to disable chemical-space filtering.
Chemical space to constrain generated molecules. Use ‘enamine_real’ for the Enamine REAL chemical space, ‘wuxi_galaxi’ for the WuXi GalaXi chemical space, or ‘none’ to disable chemical-space filtering.
Client-provided key to prevent duplicate submissions on retries
molecule_filters: optional object { boltz_smarts_catalog_filter_level, custom_filters } Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters.
Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters.
boltz_smarts_catalog_filter_level: optional "recommended" or "extra" or "aggressive" or "disabled"Controls the stringency of Boltz’s built-in SMARTS structural alert filtering, which removes molecules matching known problematic substructures. When omitted, small-molecule design and library screen use ‘recommended’, while Explore uses ‘disabled’. ‘recommended’: applies a curated set of alerts balancing safety and hit rate. ‘extra’: adds additional alerts beyond the recommended set for stricter filtering. ‘aggressive’: applies the most comprehensive alert set — may reject viable molecules. ‘disabled’: turns off Boltz SMARTS filtering entirely; only custom_filters will be applied.
Controls the stringency of Boltz’s built-in SMARTS structural alert filtering, which removes molecules matching known problematic substructures. When omitted, small-molecule design and library screen use ‘recommended’, while Explore uses ‘disabled’. ‘recommended’: applies a curated set of alerts balancing safety and hit rate. ‘extra’: adds additional alerts beyond the recommended set for stricter filtering. ‘aggressive’: applies the most comprehensive alert set — may reject viable molecules. ‘disabled’: turns off Boltz SMARTS filtering entirely; only custom_filters will be applied.
custom_filters: optional array of object { max_hba, max_hbd, max_logp, 3 more } or object { type, fraction_csp3, mol_logp, 8 more } or object { patterns, type } or 2 moreCustom filters to apply. Molecules must pass all filters (AND logic).
Custom filters to apply. Molecules must pass all filters (AND logic).
LipinskiFilterResponse object { max_hba, max_hbd, max_logp, 3 more } Lipinski’s Rule of Five filter. Rejects molecules that violate drug-likeness criteria based on molecular weight, LogP, hydrogen bond donors, and hydrogen bond acceptors.
Lipinski’s Rule of Five filter. Rejects molecules that violate drug-likeness criteria based on molecular weight, LogP, hydrogen bond donors, and hydrogen bond acceptors.
RdkitDescriptorFilterResponse object { type, fraction_csp3, mol_logp, 8 more } Filter molecules by RDKit molecular descriptors. Each descriptor is constrained to a min/max range. Only descriptors you provide are checked — omitted descriptors are unconstrained.
Filter molecules by RDKit molecular descriptors. Each descriptor is constrained to a min/max range. Only descriptors you provide are checked — omitted descriptors are unconstrained.
fraction_csp3: optional object { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
num_aromatic_rings: optional object { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
num_h_acceptors: optional object { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
num_h_donors: optional object { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
num_heteroatoms: optional object { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
SmartsCustomFilterResponse object { patterns, type } Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected.
Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected.
SmScreen object { id, completed_at, created_at, 14 more } A small molecule library screening pipeline run
A small molecule 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 { molecules, target, molecule_filters } Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
target: object { entities, bonds, constraints, 3 more } Target protein sequences for small molecule design or screening.
Target protein sequences for small molecule design or screening.
entities: array of object { chain_ids, type, value, 2 more } or object { bonds, chain_ids, residues, type } Protein and glycan entities defining the target structure. At least one protein entity is required.
Protein and glycan entities defining the target structure. At least one protein entity is required.
ProteinEntityResponse object { chain_ids, type, value, 2 more }
GlycanEntityResponse object { bonds, chain_ids, residues, type } Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
bonds: array of object { atom1, atom2 } Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
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, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
atom2: object { atom_name, chain_id, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use 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.
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 binding pocket on that chain. When provided, these residues guide pocket extraction and add a derived pocket constraint during affinity predictions. That derived constraint remains separate from any explicit pocket constraints in target.constraints. When omitted, the model auto-detects the pocket.
molecule_filters: optional object { boltz_smarts_catalog_filter_level, custom_filters } Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters.
Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters.
boltz_smarts_catalog_filter_level: optional "recommended" or "extra" or "aggressive" or "disabled"Controls the stringency of Boltz’s built-in SMARTS structural alert filtering, which removes molecules matching known problematic substructures. When omitted, small-molecule design and library screen use ‘recommended’, while Explore uses ‘disabled’. ‘recommended’: applies a curated set of alerts balancing safety and hit rate. ‘extra’: adds additional alerts beyond the recommended set for stricter filtering. ‘aggressive’: applies the most comprehensive alert set — may reject viable molecules. ‘disabled’: turns off Boltz SMARTS filtering entirely; only custom_filters will be applied.
Controls the stringency of Boltz’s built-in SMARTS structural alert filtering, which removes molecules matching known problematic substructures. When omitted, small-molecule design and library screen use ‘recommended’, while Explore uses ‘disabled’. ‘recommended’: applies a curated set of alerts balancing safety and hit rate. ‘extra’: adds additional alerts beyond the recommended set for stricter filtering. ‘aggressive’: applies the most comprehensive alert set — may reject viable molecules. ‘disabled’: turns off Boltz SMARTS filtering entirely; only custom_filters will be applied.
custom_filters: optional array of object { max_hba, max_hbd, max_logp, 3 more } or object { type, fraction_csp3, mol_logp, 8 more } or object { patterns, type } or 2 moreCustom filters to apply. Molecules must pass all filters (AND logic).
Custom filters to apply. Molecules must pass all filters (AND logic).
LipinskiFilterResponse object { max_hba, max_hbd, max_logp, 3 more } Lipinski’s Rule of Five filter. Rejects molecules that violate drug-likeness criteria based on molecular weight, LogP, hydrogen bond donors, and hydrogen bond acceptors.
Lipinski’s Rule of Five filter. Rejects molecules that violate drug-likeness criteria based on molecular weight, LogP, hydrogen bond donors, and hydrogen bond acceptors.
RdkitDescriptorFilterResponse object { type, fraction_csp3, mol_logp, 8 more } Filter molecules by RDKit molecular descriptors. Each descriptor is constrained to a min/max range. Only descriptors you provide are checked — omitted descriptors are unconstrained.
Filter molecules by RDKit molecular descriptors. Each descriptor is constrained to a min/max range. Only descriptors you provide are checked — omitted descriptors are unconstrained.
fraction_csp3: optional object { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
num_aromatic_rings: optional object { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
num_h_acceptors: optional object { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
num_h_donors: optional object { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
num_heteroatoms: optional object { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
SmartsCustomFilterResponse object { patterns, type } Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected.
Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected.
progress: object { num_molecules_failed, num_molecules_screened, total_molecules_to_screen, 2 more }
Number of accepted molecules that reached terminal failure during screening.
Number of accepted molecules that produced usable screening results.
SmExplore object { id, completed_at, created_at, 14 more } A small molecule library exploration pipeline run
A small molecule library exploration 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 { budget, library, target, molecule_filters } Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
How many molecules to score. Each is chosen using everything scored before it, so a run recovers far more of the library’s best-scoring molecules than screening the same number blindly. Scoring around 7% of the library is where that advantage is clearest. Must not exceed the accepted library size or 5,000,000.
library: object { format, smiles_column, source, id_column }
target: object { entities, bonds, constraints, 3 more } Target protein sequences for small molecule design or screening.
Target protein sequences for small molecule design or screening.
entities: array of object { chain_ids, type, value, 2 more } or object { bonds, chain_ids, residues, type } Protein and glycan entities defining the target structure. At least one protein entity is required.
Protein and glycan entities defining the target structure. At least one protein entity is required.
ProteinEntityResponse object { chain_ids, type, value, 2 more }
GlycanEntityResponse object { bonds, chain_ids, residues, type } Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
bonds: array of object { atom1, atom2 } Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
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, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
atom2: object { atom_name, chain_id, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use 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.
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 binding pocket on that chain. When provided, these residues guide pocket extraction and add a derived pocket constraint during affinity predictions. That derived constraint remains separate from any explicit pocket constraints in target.constraints. When omitted, the model auto-detects the pocket.
molecule_filters: optional object { boltz_smarts_catalog_filter_level, custom_filters } Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters.
Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters.
boltz_smarts_catalog_filter_level: optional "recommended" or "extra" or "aggressive" or "disabled"Controls the stringency of Boltz’s built-in SMARTS structural alert filtering, which removes molecules matching known problematic substructures. When omitted, small-molecule design and library screen use ‘recommended’, while Explore uses ‘disabled’. ‘recommended’: applies a curated set of alerts balancing safety and hit rate. ‘extra’: adds additional alerts beyond the recommended set for stricter filtering. ‘aggressive’: applies the most comprehensive alert set — may reject viable molecules. ‘disabled’: turns off Boltz SMARTS filtering entirely; only custom_filters will be applied.
Controls the stringency of Boltz’s built-in SMARTS structural alert filtering, which removes molecules matching known problematic substructures. When omitted, small-molecule design and library screen use ‘recommended’, while Explore uses ‘disabled’. ‘recommended’: applies a curated set of alerts balancing safety and hit rate. ‘extra’: adds additional alerts beyond the recommended set for stricter filtering. ‘aggressive’: applies the most comprehensive alert set — may reject viable molecules. ‘disabled’: turns off Boltz SMARTS filtering entirely; only custom_filters will be applied.
custom_filters: optional array of object { max_hba, max_hbd, max_logp, 3 more } or object { type, fraction_csp3, mol_logp, 8 more } or object { patterns, type } or 2 moreCustom filters to apply. Molecules must pass all filters (AND logic).
Custom filters to apply. Molecules must pass all filters (AND logic).
LipinskiFilterResponse object { max_hba, max_hbd, max_logp, 3 more } Lipinski’s Rule of Five filter. Rejects molecules that violate drug-likeness criteria based on molecular weight, LogP, hydrogen bond donors, and hydrogen bond acceptors.
Lipinski’s Rule of Five filter. Rejects molecules that violate drug-likeness criteria based on molecular weight, LogP, hydrogen bond donors, and hydrogen bond acceptors.
RdkitDescriptorFilterResponse object { type, fraction_csp3, mol_logp, 8 more } Filter molecules by RDKit molecular descriptors. Each descriptor is constrained to a min/max range. Only descriptors you provide are checked — omitted descriptors are unconstrained.
Filter molecules by RDKit molecular descriptors. Each descriptor is constrained to a min/max range. Only descriptors you provide are checked — omitted descriptors are unconstrained.
fraction_csp3: optional object { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
num_aromatic_rings: optional object { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
num_h_acceptors: optional object { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
num_h_donors: optional object { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
num_heteroatoms: optional object { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
SmartsCustomFilterResponse object { patterns, type } Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected.
Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected.
progress: object { num_molecules_failed, num_molecules_scored, phase, 4 more }
Molecules that reached terminal failure. These do not consume budget — each is replaced by another selection.
Molecules that produced a usable result. The run completes when this reaches the budget.
phase: "preparing_library" or "building_graph" or "scoring"Stage of the run: preparing_library while the submitted library is fetched, validated and de-duplicated; building_graph while the neighbor graph and target inputs are prepared; scoring once molecules are being selected and scored. Phases only move forward, and a resumed run does not repeat one it has finished.
Stage of the run: preparing_library while the submitted library is fetched, validated and de-duplicated; building_graph while the neighbor graph and target inputs are prepared; scoring once molecules are being selected and scored. Phases only move forward, and a resumed run does not repeat one it has finished.
The requested budget: how many of the library will be scored.
Distinct molecules accepted after validation, filtering and de-duplication. Omitted while the submitted library is being prepared.
predictions: array of object { id, completed_at, created_at, 12 more } or object { id, completed_at, created_at, 12 more } Predictions exposed by this share link, in the order they were registered.
Predictions exposed by this share link, in the order they were registered.
Boltz2Prediction object { id, completed_at, created_at, 12 more }
When the input/output data was deleted, or null if still available
When this resource and its associated data will be permanently deleted. Null while still in progress.
input: object { entities, binding, bonds, 4 more } Prediction input (null if data deleted)
Prediction input (null if data deleted)
entities: array of object { chain_ids, type, value, 3 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 3 moreEntities (proteins, RNA, DNA, ligands, and glycans) forming the complex to predict. Order determines chain assignment.
Entities (proteins, RNA, DNA, ligands, and glycans) forming the complex to predict. Order determines chain assignment.
Boltz2ProteinEntityResponse object { chain_ids, type, value, 3 more }
modifications: optional array of object { residue_index, type, value } CCD post-translational modifications. Optional; defaults to an empty list when omitted. SMILES modifications are not supported.
CCD post-translational modifications. Optional; defaults to an empty list when omitted. SMILES modifications are not supported.
msa: optional object { format, source, type } or object { type } Optional protein MSA control. Omit msa on all protein entities to use automatic MSA generation. Use custom for user-provided A3M/CSV files, or empty for single-sequence mode. Custom MSA and automatic MSA cannot be mixed in one request.
Optional protein MSA control. Omit msa on all protein entities to use automatic MSA generation. Use custom for user-provided A3M/CSV files, or empty for single-sequence mode. Custom MSA and automatic MSA cannot be mixed in one request.
Boltz2CustomMsaResponse object { format, source, type } Use a user-provided MSA for this protein entity. If any protein entity uses a custom MSA, every other protein entity must use either custom or empty MSA; automatic MSA generation cannot be mixed with custom MSAs in the same request.
Use a user-provided MSA for this protein entity. If any protein entity uses a custom MSA, every other protein entity must use either custom or empty MSA; automatic MSA generation cannot be mixed with custom MSAs in the same request.
RnaEntityResponse object { chain_ids, type, value, 2 more }
DnaEntityResponse object { chain_ids, type, value, 2 more }
GlycanEntityResponse object { bonds, chain_ids, residues, type } Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
bonds: array of object { atom1, atom2 } Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
binding: optional object { binder_chain_id, type } or object { binder_chain_ids, type }
bonds: optional array of object { atom1, atom2 } Request-level covalent bonds between atoms. Use ccd_atom with a glycan residue ID, smiles_atom with a numeric SMILES atom-map, or ligand_atom for a single-residue ligand. Internal glycan bonds belong in the glycan entity bonds field.
Request-level covalent bonds between atoms. Use ccd_atom with a glycan residue ID, smiles_atom with a numeric SMILES atom-map, or ligand_atom for a single-residue ligand. Internal glycan bonds belong in the glycan entity bonds field.
atom1: object { atom_name, chain_id, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
atom2: object { atom_name, chain_id, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use 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.
model_options: optional object { recycling_steps, sampling_steps, seed, step_scale }
The number of recycling steps to use for prediction. Default is 3.
The number of sampling steps to use for prediction. Default is 200.
templates: optional array of object { template_chains, template_structure, force_threshold_angstroms } Template structure files to guide protein-chain prediction. Supports up to 4 CIF or PDB templates from HTTPS URLs or base64 uploads. Use template_chains to map request chains to template-file chains.
Template structure files to guide protein-chain prediction. Supports up to 4 CIF or PDB templates from HTTPS URLs or base64 uploads. Use template_chains to map request chains to template-file chains.
output: object { all_sample_results, best_sample, archive, binding_metrics } Prediction output when succeeded
Prediction output when succeeded
all_sample_results: array of object { metrics, structure, ligand_structure } Per-sample structure results
Per-sample structure results
best_sample: object { metrics, structure, ligand_structure }
AdmePrediction object { id, completed_at, created_at, 12 more }
When the input/output data was deleted, or null if still available
When this resource and its associated data will be permanently deleted. Null while still in progress.
input: object { molecules } Prediction input (null if data deleted)
Prediction input (null if data deleted)
output: object { molecules } Prediction output when succeeded
Prediction output when succeeded
molecules: array of object { id, adme, error, 3 more } or object { id, adme, error, 3 more } Per-molecule results in the same order as the request. Successful molecules carry an adme summary. Failed molecules carry status: "failed" and a non-null error.
Per-molecule results in the same order as the request. Successful molecules carry an adme summary. Failed molecules carry status: "failed" and a non-null error.
ShareLinkListPipelineResultsResponse 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 3 moreDesigned and fixed entities returned for this result.
Designed and fixed entities returned for this result.
ProteinEntity object { chain_ids, type, value, 2 more }
RnaEntity object { chain_ids, type, value, 2 more }
DnaEntity object { chain_ids, type, value, 2 more }
GlycanEntity object { bonds, chain_ids, residues, type } Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
Branched glycan represented as an explicit graph of CCD monosaccharide residues. Declare internal connectivity in this entity and cross-entity attachments in the request-level bonds array.
bonds: array of object { atom1, atom2 } Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
Internal covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
metrics: object { binding_confidence, helix_fraction, iptm, 6 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).
Minimum predicted aligned error at the interface (Angstroms). Lower values indicate higher confidence.