# Sequence Redesign ## Start a protein sequence redesign run `$ boltz-api protein:sequence-redesign start` **post** `/compute/v1/protein/sequence-redesign` Create a protein sequence redesign run from selected residues in a fixed input structure ### Parameters - `--entity: 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. - `--num-proteins: number` Number of unique filter-passing redesigned proteins to generate. - `--structure: object { type, url } or object { data, media_type, type }` How to provide a CIF structure file. URLs are auto-detected; base64 uploads must use chemical/x-cif media type. - `--type: "binder"` - `--global-design-filter: 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. - `--idempotency-key: optional string` - `--workspace-id: optional string` Workspace to run this redesign in. ### Returns - `ProteinSequenceRedesignStartResponse: object { id, completed_at, created_at, 14 more }` A fixed-structure protein sequence redesign run. - `id: string` Unique ProteinSequenceRedesignRun identifier - `completed_at: string` - `created_at: string` - `data_deleted_at: string` When the input, output, and result data was permanently deleted. Null if data has not been deleted. - `engine: "boltz-protein-redesign"` Deprecated. Use pipeline instead. - `engine_version: "v2026-07-14"` Deprecated. Use pipeline_version instead. - `error: object { code, message, details }` - `code: string` Machine-readable error code - `message: string` Human-readable error message - `details: optional unknown` Additional field-level error details keyed by input path, when available. - `input: object { entities, num_proteins, structure, 4 more } or object { entities, num_proteins, structure, 4 more }` 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. - `BinderSequenceRedesignTargetEntityResponse: object { chain_id, role, type }` A fixed target chain from the input CIF. - `chain_id: string` - `role: "target"` - `type: "from_template"` - `BinderSequenceRedesignBinderEntityResponse: object { chain_id, role, type, design_motifs }` - `chain_id: string` - `role: "binder"` - `type: "from_template"` - `design_motifs: optional array of object { filters, residues, type }` 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. - `ExcludedAminoAcidsDesignFilterResponse: object { amino_acids, type }` - `amino_acids: array of string` Single-letter amino-acid codes that must not occur in the filtered designed region. - `type: "excluded_amino_acids"` - `MaxHydrophobicFractionDesignFilterResponse: object { max_fraction, type }` - `max_fraction: number` - `type: "max_hydrophobic_fraction"` - `ExcludedSequenceMotifsDesignFilterResponse: object { motifs, type }` - `motifs: array of string` Sequence motifs that must not occur. X matches any single residue. - `type: "excluded_sequence_motifs"` - `residues: array of number` 0-indexed residues to redesign on this chain. - `type: "residues"` - `num_proteins: number` Number of unique filter-passing redesigned proteins to generate. - `structure: object { url, url_expires_at }` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `type: "binder"` - `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. - `ExcludedAminoAcidsDesignFilterResponse: object { amino_acids, type }` - `amino_acids: array of string` Single-letter amino-acid codes that must not occur in the filtered designed region. - `type: "excluded_amino_acids"` - `MaxHydrophobicFractionDesignFilterResponse: object { max_fraction, type }` - `max_fraction: number` - `type: "max_hydrophobic_fraction"` - `ExcludedSequenceMotifsDesignFilterResponse: object { motifs, type }` - `motifs: array of string` Sequence motifs that must not occur. X matches any single residue. - `type: "excluded_sequence_motifs"` - `idempotency_key: optional string` - `workspace_id: optional string` Workspace to run this redesign in. - `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. - `chain_id: string` - `type: "from_template"` - `design_motifs: optional array of object { filters, residues, type }` 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. - `ExcludedAminoAcidsDesignFilterResponse: object { amino_acids, type }` - `amino_acids: array of string` Single-letter amino-acid codes that must not occur in the filtered designed region. - `type: "excluded_amino_acids"` - `MaxHydrophobicFractionDesignFilterResponse: object { max_fraction, type }` - `max_fraction: number` - `type: "max_hydrophobic_fraction"` - `ExcludedSequenceMotifsDesignFilterResponse: object { motifs, type }` - `motifs: array of string` Sequence motifs that must not occur. X matches any single residue. - `type: "excluded_sequence_motifs"` - `residues: array of number` 0-indexed residues to redesign on this chain. - `type: "residues"` - `num_proteins: number` Number of unique filter-passing redesigned proteins to generate. - `structure: object { url, url_expires_at }` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `type: "generic"` - `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. - `ExcludedAminoAcidsDesignFilterResponse: object { amino_acids, type }` - `amino_acids: array of string` Single-letter amino-acid codes that must not occur in the filtered designed region. - `type: "excluded_amino_acids"` - `MaxHydrophobicFractionDesignFilterResponse: object { max_fraction, type }` - `max_fraction: number` - `type: "max_hydrophobic_fraction"` - `ExcludedSequenceMotifsDesignFilterResponse: object { motifs, type }` - `motifs: array of string` Sequence motifs that must not occur. X matches any single residue. - `type: "excluded_sequence_motifs"` - `idempotency_key: optional string` - `workspace_id: optional string` Workspace to run this redesign in. - `livemode: boolean` Whether this resource was created with a live API key. - `pipeline: "boltz-protein-redesign"` - `pipeline_version: "v2026-07-14"` - `progress: object { num_proteins_generated, total_proteins_to_generate, latest_result_id }` - `num_proteins_generated: number` Number of protein binders generated so far - `total_proteins_to_generate: number` Total number of protein binders requested - `latest_result_id: optional string` ID of the most recently generated result - `started_at: string` - `status: "pending" or "running" or "succeeded" or 2 more` - `"pending"` - `"running"` - `"succeeded"` - `"failed"` - `"stopped"` - `stopped_at: string` - `workspace_id: string` Workspace ID - `idempotency_key: optional string` Client-provided idempotency key ### Example ```cli boltz-api protein:sequence-redesign start \ --api-key 'My API Key' \ --entity '{chain_id: x, role: target, type: from_template}' \ --entity '{chain_id: x, role: target, type: from_template}' \ --num-proteins 1 \ --structure '{type: url, url: https://example.com}' \ --type binder ``` #### Response ```json { "id": "id", "completed_at": "2019-12-27T18:11:19.117Z", "created_at": "2019-12-27T18:11:19.117Z", "data_deleted_at": "2019-12-27T18:11:19.117Z", "engine": "boltz-protein-redesign", "engine_version": "v2026-07-14", "error": { "code": "code", "message": "message", "details": {} }, "input": { "entities": [ { "chain_id": "x", "role": "target", "type": "from_template" }, { "chain_id": "x", "role": "target", "type": "from_template" } ], "num_proteins": 1, "structure": { "url": "https://example.com", "url_expires_at": "2019-12-27T18:11:19.117Z" }, "type": "binder", "global_design_filters": [ { "amino_acids": [ "x" ], "type": "excluded_amino_acids" } ], "idempotency_key": "idempotency_key", "workspace_id": "workspace_id" }, "livemode": true, "pipeline": "boltz-protein-redesign", "pipeline_version": "v2026-07-14", "progress": { "num_proteins_generated": 0, "total_proteins_to_generate": 1, "latest_result_id": "latest_result_id" }, "started_at": "2019-12-27T18:11:19.117Z", "status": "pending", "stopped_at": "2019-12-27T18:11:19.117Z", "workspace_id": "workspace_id", "idempotency_key": "idempotency_key" } ``` ## List protein sequence redesign runs `$ boltz-api protein:sequence-redesign list` **get** `/compute/v1/protein/sequence-redesign` List protein sequence redesign runs, optionally filtered by workspace ### Parameters - `--after-id: optional string` Return results after this ID - `--before-id: optional string` Return results before this ID - `--limit: optional number` Max items to return. Defaults to 100. - `--workspace-id: optional string` Filter by workspace ID. Only used with admin API keys. If not provided, defaults to the workspace associated with the API key, or the default workspace for admin keys. ### Returns - `ListProteinSequenceRedesignRunsResponse: object { data, first_id, has_more, last_id }` - `data: array of object { id, completed_at, created_at, 13 more }` - `id: string` Unique ProteinSequenceRedesignRunSummary identifier - `completed_at: string` - `created_at: string` - `data_deleted_at: string` When the input, output, and result data was permanently deleted. Null if data has not been deleted. - `engine: "boltz-protein-redesign"` Deprecated. Use pipeline instead. - `engine_version: "v2026-07-14"` Deprecated. Use pipeline_version instead. - `error: object { code, message, details }` - `code: string` Machine-readable error code - `message: string` Human-readable error message - `details: optional unknown` Additional field-level error details keyed by input path, when available. - `livemode: boolean` Whether this resource was created with a live API key. - `pipeline: "boltz-protein-redesign"` - `pipeline_version: "v2026-07-14"` - `progress: object { num_proteins_generated, total_proteins_to_generate, latest_result_id }` - `num_proteins_generated: number` Number of protein binders generated so far - `total_proteins_to_generate: number` Total number of protein binders requested - `latest_result_id: optional string` ID of the most recently generated result - `started_at: string` - `status: "pending" or "running" or "succeeded" or 2 more` - `"pending"` - `"running"` - `"succeeded"` - `"failed"` - `"stopped"` - `stopped_at: string` - `workspace_id: string` Workspace ID - `idempotency_key: optional string` Client-provided idempotency key - `first_id: string` ID of the first item. Use as before_id for the previous page. - `has_more: boolean` - `last_id: string` ID of the last item. Use as after_id for the next page. ### Example ```cli boltz-api protein:sequence-redesign list \ --api-key 'My API Key' ``` #### Response ```json { "data": [ { "id": "id", "completed_at": "2019-12-27T18:11:19.117Z", "created_at": "2019-12-27T18:11:19.117Z", "data_deleted_at": "2019-12-27T18:11:19.117Z", "engine": "boltz-protein-redesign", "engine_version": "v2026-07-14", "error": { "code": "code", "message": "message", "details": {} }, "livemode": true, "pipeline": "boltz-protein-redesign", "pipeline_version": "v2026-07-14", "progress": { "num_proteins_generated": 0, "total_proteins_to_generate": 1, "latest_result_id": "latest_result_id" }, "started_at": "2019-12-27T18:11:19.117Z", "status": "pending", "stopped_at": "2019-12-27T18:11:19.117Z", "workspace_id": "workspace_id", "idempotency_key": "idempotency_key" } ], "first_id": "first_id", "has_more": true, "last_id": "last_id" } ``` ## Get protein sequence redesign run status `$ boltz-api protein:sequence-redesign retrieve` **get** `/compute/v1/protein/sequence-redesign/{id}` Retrieve a sequence redesign run by ID, including progress and status ### Parameters - `--id: string` Sequence redesign run ID - `--workspace-id: optional string` Workspace ID. Only used with admin API keys. Ignored (or validated) for workspace-scoped keys. ### Returns - `ProteinSequenceRedesignGetResponse: object { id, completed_at, created_at, 14 more }` A fixed-structure protein sequence redesign run. - `id: string` Unique ProteinSequenceRedesignRun identifier - `completed_at: string` - `created_at: string` - `data_deleted_at: string` When the input, output, and result data was permanently deleted. Null if data has not been deleted. - `engine: "boltz-protein-redesign"` Deprecated. Use pipeline instead. - `engine_version: "v2026-07-14"` Deprecated. Use pipeline_version instead. - `error: object { code, message, details }` - `code: string` Machine-readable error code - `message: string` Human-readable error message - `details: optional unknown` Additional field-level error details keyed by input path, when available. - `input: object { entities, num_proteins, structure, 4 more } or object { entities, num_proteins, structure, 4 more }` 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. - `BinderSequenceRedesignTargetEntityResponse: object { chain_id, role, type }` A fixed target chain from the input CIF. - `chain_id: string` - `role: "target"` - `type: "from_template"` - `BinderSequenceRedesignBinderEntityResponse: object { chain_id, role, type, design_motifs }` - `chain_id: string` - `role: "binder"` - `type: "from_template"` - `design_motifs: optional array of object { filters, residues, type }` 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. - `ExcludedAminoAcidsDesignFilterResponse: object { amino_acids, type }` - `amino_acids: array of string` Single-letter amino-acid codes that must not occur in the filtered designed region. - `type: "excluded_amino_acids"` - `MaxHydrophobicFractionDesignFilterResponse: object { max_fraction, type }` - `max_fraction: number` - `type: "max_hydrophobic_fraction"` - `ExcludedSequenceMotifsDesignFilterResponse: object { motifs, type }` - `motifs: array of string` Sequence motifs that must not occur. X matches any single residue. - `type: "excluded_sequence_motifs"` - `residues: array of number` 0-indexed residues to redesign on this chain. - `type: "residues"` - `num_proteins: number` Number of unique filter-passing redesigned proteins to generate. - `structure: object { url, url_expires_at }` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `type: "binder"` - `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. - `ExcludedAminoAcidsDesignFilterResponse: object { amino_acids, type }` - `amino_acids: array of string` Single-letter amino-acid codes that must not occur in the filtered designed region. - `type: "excluded_amino_acids"` - `MaxHydrophobicFractionDesignFilterResponse: object { max_fraction, type }` - `max_fraction: number` - `type: "max_hydrophobic_fraction"` - `ExcludedSequenceMotifsDesignFilterResponse: object { motifs, type }` - `motifs: array of string` Sequence motifs that must not occur. X matches any single residue. - `type: "excluded_sequence_motifs"` - `idempotency_key: optional string` - `workspace_id: optional string` Workspace to run this redesign in. - `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. - `chain_id: string` - `type: "from_template"` - `design_motifs: optional array of object { filters, residues, type }` 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. - `ExcludedAminoAcidsDesignFilterResponse: object { amino_acids, type }` - `amino_acids: array of string` Single-letter amino-acid codes that must not occur in the filtered designed region. - `type: "excluded_amino_acids"` - `MaxHydrophobicFractionDesignFilterResponse: object { max_fraction, type }` - `max_fraction: number` - `type: "max_hydrophobic_fraction"` - `ExcludedSequenceMotifsDesignFilterResponse: object { motifs, type }` - `motifs: array of string` Sequence motifs that must not occur. X matches any single residue. - `type: "excluded_sequence_motifs"` - `residues: array of number` 0-indexed residues to redesign on this chain. - `type: "residues"` - `num_proteins: number` Number of unique filter-passing redesigned proteins to generate. - `structure: object { url, url_expires_at }` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `type: "generic"` - `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. - `ExcludedAminoAcidsDesignFilterResponse: object { amino_acids, type }` - `amino_acids: array of string` Single-letter amino-acid codes that must not occur in the filtered designed region. - `type: "excluded_amino_acids"` - `MaxHydrophobicFractionDesignFilterResponse: object { max_fraction, type }` - `max_fraction: number` - `type: "max_hydrophobic_fraction"` - `ExcludedSequenceMotifsDesignFilterResponse: object { motifs, type }` - `motifs: array of string` Sequence motifs that must not occur. X matches any single residue. - `type: "excluded_sequence_motifs"` - `idempotency_key: optional string` - `workspace_id: optional string` Workspace to run this redesign in. - `livemode: boolean` Whether this resource was created with a live API key. - `pipeline: "boltz-protein-redesign"` - `pipeline_version: "v2026-07-14"` - `progress: object { num_proteins_generated, total_proteins_to_generate, latest_result_id }` - `num_proteins_generated: number` Number of protein binders generated so far - `total_proteins_to_generate: number` Total number of protein binders requested - `latest_result_id: optional string` ID of the most recently generated result - `started_at: string` - `status: "pending" or "running" or "succeeded" or 2 more` - `"pending"` - `"running"` - `"succeeded"` - `"failed"` - `"stopped"` - `stopped_at: string` - `workspace_id: string` Workspace ID - `idempotency_key: optional string` Client-provided idempotency key ### Example ```cli boltz-api protein:sequence-redesign retrieve \ --api-key 'My API Key' \ --id id ``` #### Response ```json { "id": "id", "completed_at": "2019-12-27T18:11:19.117Z", "created_at": "2019-12-27T18:11:19.117Z", "data_deleted_at": "2019-12-27T18:11:19.117Z", "engine": "boltz-protein-redesign", "engine_version": "v2026-07-14", "error": { "code": "code", "message": "message", "details": {} }, "input": { "entities": [ { "chain_id": "x", "role": "target", "type": "from_template" }, { "chain_id": "x", "role": "target", "type": "from_template" } ], "num_proteins": 1, "structure": { "url": "https://example.com", "url_expires_at": "2019-12-27T18:11:19.117Z" }, "type": "binder", "global_design_filters": [ { "amino_acids": [ "x" ], "type": "excluded_amino_acids" } ], "idempotency_key": "idempotency_key", "workspace_id": "workspace_id" }, "livemode": true, "pipeline": "boltz-protein-redesign", "pipeline_version": "v2026-07-14", "progress": { "num_proteins_generated": 0, "total_proteins_to_generate": 1, "latest_result_id": "latest_result_id" }, "started_at": "2019-12-27T18:11:19.117Z", "status": "pending", "stopped_at": "2019-12-27T18:11:19.117Z", "workspace_id": "workspace_id", "idempotency_key": "idempotency_key" } ``` ## Get redesigned protein sequences `$ boltz-api protein:sequence-redesign list-results` **get** `/compute/v1/protein/sequence-redesign/{id}/results` Retrieve paginated results from a protein sequence redesign run ### Parameters - `--id: string` Sequence redesign run ID - `--after-id: optional string` Return results after this ID - `--before-id: optional string` Return results before this ID - `--ids: optional string` Comma-separated list of result IDs to filter by (max 200). Only results whose ID matches one of these is returned; missing IDs are silently skipped. Composes with `limit`, `after_id`, and `before_id` — the filter is applied before pagination. - `--limit: optional number` Max results to return. Defaults to 100. - `--workspace-id: optional string` Workspace ID. Only used with admin API keys. Ignored (or validated) for workspace-scoped keys. ### Returns - `ProteinSequenceRedesignResultsResponse: object { data, first_id, has_more, last_id }` - `data: array of object { id, artifacts, created_at, 4 more } or object { id, artifacts, created_at, 4 more }` - `BinderProteinDesignResult: object { id, artifacts, created_at, 4 more }` - `id: string` Unique result ID. - `artifacts: object { archive, structure }` - `archive: object { url, url_expires_at }` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `structure: optional object { url, url_expires_at }` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `created_at: string` - `entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 2 more` Entities in the designed complex, including designed and fixed input entities. - `ProteinEntity: object { chain_ids, type, value, 2 more }` - `chain_ids: array of string` Chain IDs for this entity - `type: "protein"` - `value: string` Amino acid sequence (one-letter codes) - `cyclic: optional boolean` Whether the sequence is cyclic - `modifications: optional array of object { residue_index, type, value }` CCD post-translational modifications. Optional; defaults to an empty list when omitted. SMILES modifications are not supported. - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` Modification format. Only CCD polymer modifications are supported. - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `RNAEntity: object { chain_ids, type, value, 2 more }` - `chain_ids: array of string` Chain IDs for this entity - `type: "rna"` - `value: string` RNA nucleotide sequence (A, C, G, U, N) - `cyclic: optional boolean` Whether the sequence is cyclic - `modifications: optional array of object { residue_index, type, value }` CCD chemical modifications. Optional; defaults to an empty list when omitted. SMILES modifications are not supported. - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` Modification format. Only CCD polymer modifications are supported. - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `DNAEntity: object { chain_ids, type, value, 2 more }` - `chain_ids: array of string` Chain IDs for this entity - `type: "dna"` - `value: string` DNA nucleotide sequence (A, C, G, T, N) - `cyclic: optional boolean` Whether the sequence is cyclic - `modifications: optional array of object { residue_index, type, value }` CCD chemical modifications. Optional; defaults to an empty list when omitted. SMILES modifications are not supported. - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` Modification format. Only CCD polymer modifications are supported. - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `LigandCCDEntity: object { chain_ids, type, value }` - `chain_ids: array of string` Chain IDs for this ligand - `type: "ligand_ccd"` - `value: string` CCD code (e.g., ATP, ADP) - `LigandSmilesEntity: object { chain_ids, type, value }` - `chain_ids: array of string` Chain IDs for this ligand - `type: "ligand_smiles"` - `value: string` SMILES string representing the ligand - `metrics: object { binding_confidence, helix_fraction, iptm, 4 more }` Structural and binding quality metrics for a designed protein binder - `binding_confidence: number` Confidence that the designed binder binds the target (0-1). Primary metric for hit discovery. - `helix_fraction: number` Fraction of the designed sequence forming alpha helices (0-1). - `iptm: number` Interface predicted TM score (0-1). Confidence in the protein-protein interface. - `loop_fraction: number` Fraction of the designed sequence in coil/loop regions (0-1). - `min_interaction_pae: number` Minimum predicted aligned error at the interface (Angstroms). Lower values indicate higher confidence. - `sheet_fraction: number` Fraction of the designed sequence forming beta sheets (0-1). - `structure_confidence: number` Confidence in the predicted 3D structure (0-1). - `type: "binder"` - `warnings: optional array of object { code, message }` Warnings about potential quality issues with this result. - `code: string` Machine-readable warning code (e.g. "low_confidence", "unusual_geometry") - `message: string` Human-readable description of the warning - `GenericProteinDesignResult: object { id, artifacts, created_at, 4 more }` - `id: string` Unique result ID. - `artifacts: object { archive, structure }` - `archive: object { url, url_expires_at }` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `structure: optional object { url, url_expires_at }` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `created_at: string` - `entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 2 more` Entities in the designed complex, including designed and fixed input entities. - `ProteinEntity: object { chain_ids, type, value, 2 more }` - `chain_ids: array of string` Chain IDs for this entity - `type: "protein"` - `value: string` Amino acid sequence (one-letter codes) - `cyclic: optional boolean` Whether the sequence is cyclic - `modifications: optional array of object { residue_index, type, value }` CCD post-translational modifications. Optional; defaults to an empty list when omitted. SMILES modifications are not supported. - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` Modification format. Only CCD polymer modifications are supported. - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `RNAEntity: object { chain_ids, type, value, 2 more }` - `chain_ids: array of string` Chain IDs for this entity - `type: "rna"` - `value: string` RNA nucleotide sequence (A, C, G, U, N) - `cyclic: optional boolean` Whether the sequence is cyclic - `modifications: optional array of object { residue_index, type, value }` CCD chemical modifications. Optional; defaults to an empty list when omitted. SMILES modifications are not supported. - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` Modification format. Only CCD polymer modifications are supported. - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `DNAEntity: object { chain_ids, type, value, 2 more }` - `chain_ids: array of string` Chain IDs for this entity - `type: "dna"` - `value: string` DNA nucleotide sequence (A, C, G, T, N) - `cyclic: optional boolean` Whether the sequence is cyclic - `modifications: optional array of object { residue_index, type, value }` CCD chemical modifications. Optional; defaults to an empty list when omitted. SMILES modifications are not supported. - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` Modification format. Only CCD polymer modifications are supported. - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `LigandCCDEntity: object { chain_ids, type, value }` - `chain_ids: array of string` Chain IDs for this ligand - `type: "ligand_ccd"` - `value: string` CCD code (e.g., ATP, ADP) - `LigandSmilesEntity: object { chain_ids, type, value }` - `chain_ids: array of string` Chain IDs for this ligand - `type: "ligand_smiles"` - `value: string` SMILES string representing the ligand - `metrics: object { helix_fraction, loop_fraction, sheet_fraction, structure_confidence }` Structure and design-quality metrics for a generic protein design. - `helix_fraction: number` Fraction of the designed sequence forming alpha helices (0-1). - `loop_fraction: number` Fraction of the designed sequence in coil/loop regions (0-1). - `sheet_fraction: number` Fraction of the designed sequence forming beta sheets (0-1). - `structure_confidence: number` Confidence in the predicted 3D structure (0-1). - `type: "generic"` - `warnings: optional array of object { code, message }` Warnings about potential quality issues with this result. - `code: string` Machine-readable warning code (e.g. "low_confidence", "unusual_geometry") - `message: string` Human-readable description of the warning - `first_id: string` ID of the first item. Use as before_id for the previous page. - `has_more: boolean` - `last_id: string` ID of the last item. Use as after_id for the next page. ### Example ```cli boltz-api protein:sequence-redesign list-results \ --api-key 'My API Key' \ --id id ``` #### Response ```json { "data": [ { "id": "id", "artifacts": { "archive": { "url": "https://example.com", "url_expires_at": "2019-12-27T18:11:19.117Z" }, "structure": { "url": "https://example.com", "url_expires_at": "2019-12-27T18:11:19.117Z" } }, "created_at": "2019-12-27T18:11:19.117Z", "entities": [ { "chain_ids": [ "string" ], "type": "protein", "value": "value", "cyclic": true, "modifications": [ { "residue_index": 0, "type": "ccd", "value": "value" } ] } ], "metrics": { "binding_confidence": 0, "helix_fraction": 0, "iptm": 0, "loop_fraction": 0, "min_interaction_pae": 0, "sheet_fraction": 0, "structure_confidence": 0 }, "type": "binder", "warnings": [ { "code": "code", "message": "message" } ] } ], "first_id": "first_id", "has_more": true, "last_id": "last_id" } ``` ## Stop a running protein sequence redesign run `$ boltz-api protein:sequence-redesign stop` **post** `/compute/v1/protein/sequence-redesign/{id}/stop` Stop an in-progress protein sequence redesign run early ### Parameters - `--id: string` Sequence redesign run ID ### Returns - `ProteinSequenceRedesignStopResponse: object { id, completed_at, created_at, 14 more }` A fixed-structure protein sequence redesign run. - `id: string` Unique ProteinSequenceRedesignRun identifier - `completed_at: string` - `created_at: string` - `data_deleted_at: string` When the input, output, and result data was permanently deleted. Null if data has not been deleted. - `engine: "boltz-protein-redesign"` Deprecated. Use pipeline instead. - `engine_version: "v2026-07-14"` Deprecated. Use pipeline_version instead. - `error: object { code, message, details }` - `code: string` Machine-readable error code - `message: string` Human-readable error message - `details: optional unknown` Additional field-level error details keyed by input path, when available. - `input: object { entities, num_proteins, structure, 4 more } or object { entities, num_proteins, structure, 4 more }` 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. - `BinderSequenceRedesignTargetEntityResponse: object { chain_id, role, type }` A fixed target chain from the input CIF. - `chain_id: string` - `role: "target"` - `type: "from_template"` - `BinderSequenceRedesignBinderEntityResponse: object { chain_id, role, type, design_motifs }` - `chain_id: string` - `role: "binder"` - `type: "from_template"` - `design_motifs: optional array of object { filters, residues, type }` 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. - `ExcludedAminoAcidsDesignFilterResponse: object { amino_acids, type }` - `amino_acids: array of string` Single-letter amino-acid codes that must not occur in the filtered designed region. - `type: "excluded_amino_acids"` - `MaxHydrophobicFractionDesignFilterResponse: object { max_fraction, type }` - `max_fraction: number` - `type: "max_hydrophobic_fraction"` - `ExcludedSequenceMotifsDesignFilterResponse: object { motifs, type }` - `motifs: array of string` Sequence motifs that must not occur. X matches any single residue. - `type: "excluded_sequence_motifs"` - `residues: array of number` 0-indexed residues to redesign on this chain. - `type: "residues"` - `num_proteins: number` Number of unique filter-passing redesigned proteins to generate. - `structure: object { url, url_expires_at }` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `type: "binder"` - `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. - `ExcludedAminoAcidsDesignFilterResponse: object { amino_acids, type }` - `amino_acids: array of string` Single-letter amino-acid codes that must not occur in the filtered designed region. - `type: "excluded_amino_acids"` - `MaxHydrophobicFractionDesignFilterResponse: object { max_fraction, type }` - `max_fraction: number` - `type: "max_hydrophobic_fraction"` - `ExcludedSequenceMotifsDesignFilterResponse: object { motifs, type }` - `motifs: array of string` Sequence motifs that must not occur. X matches any single residue. - `type: "excluded_sequence_motifs"` - `idempotency_key: optional string` - `workspace_id: optional string` Workspace to run this redesign in. - `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. - `chain_id: string` - `type: "from_template"` - `design_motifs: optional array of object { filters, residues, type }` 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. - `ExcludedAminoAcidsDesignFilterResponse: object { amino_acids, type }` - `amino_acids: array of string` Single-letter amino-acid codes that must not occur in the filtered designed region. - `type: "excluded_amino_acids"` - `MaxHydrophobicFractionDesignFilterResponse: object { max_fraction, type }` - `max_fraction: number` - `type: "max_hydrophobic_fraction"` - `ExcludedSequenceMotifsDesignFilterResponse: object { motifs, type }` - `motifs: array of string` Sequence motifs that must not occur. X matches any single residue. - `type: "excluded_sequence_motifs"` - `residues: array of number` 0-indexed residues to redesign on this chain. - `type: "residues"` - `num_proteins: number` Number of unique filter-passing redesigned proteins to generate. - `structure: object { url, url_expires_at }` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `type: "generic"` - `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. - `ExcludedAminoAcidsDesignFilterResponse: object { amino_acids, type }` - `amino_acids: array of string` Single-letter amino-acid codes that must not occur in the filtered designed region. - `type: "excluded_amino_acids"` - `MaxHydrophobicFractionDesignFilterResponse: object { max_fraction, type }` - `max_fraction: number` - `type: "max_hydrophobic_fraction"` - `ExcludedSequenceMotifsDesignFilterResponse: object { motifs, type }` - `motifs: array of string` Sequence motifs that must not occur. X matches any single residue. - `type: "excluded_sequence_motifs"` - `idempotency_key: optional string` - `workspace_id: optional string` Workspace to run this redesign in. - `livemode: boolean` Whether this resource was created with a live API key. - `pipeline: "boltz-protein-redesign"` - `pipeline_version: "v2026-07-14"` - `progress: object { num_proteins_generated, total_proteins_to_generate, latest_result_id }` - `num_proteins_generated: number` Number of protein binders generated so far - `total_proteins_to_generate: number` Total number of protein binders requested - `latest_result_id: optional string` ID of the most recently generated result - `started_at: string` - `status: "pending" or "running" or "succeeded" or 2 more` - `"pending"` - `"running"` - `"succeeded"` - `"failed"` - `"stopped"` - `stopped_at: string` - `workspace_id: string` Workspace ID - `idempotency_key: optional string` Client-provided idempotency key ### Example ```cli boltz-api protein:sequence-redesign stop \ --api-key 'My API Key' \ --id id ``` #### Response ```json { "id": "id", "completed_at": "2019-12-27T18:11:19.117Z", "created_at": "2019-12-27T18:11:19.117Z", "data_deleted_at": "2019-12-27T18:11:19.117Z", "engine": "boltz-protein-redesign", "engine_version": "v2026-07-14", "error": { "code": "code", "message": "message", "details": {} }, "input": { "entities": [ { "chain_id": "x", "role": "target", "type": "from_template" }, { "chain_id": "x", "role": "target", "type": "from_template" } ], "num_proteins": 1, "structure": { "url": "https://example.com", "url_expires_at": "2019-12-27T18:11:19.117Z" }, "type": "binder", "global_design_filters": [ { "amino_acids": [ "x" ], "type": "excluded_amino_acids" } ], "idempotency_key": "idempotency_key", "workspace_id": "workspace_id" }, "livemode": true, "pipeline": "boltz-protein-redesign", "pipeline_version": "v2026-07-14", "progress": { "num_proteins_generated": 0, "total_proteins_to_generate": 1, "latest_result_id": "latest_result_id" }, "started_at": "2019-12-27T18:11:19.117Z", "status": "pending", "stopped_at": "2019-12-27T18:11:19.117Z", "workspace_id": "workspace_id", "idempotency_key": "idempotency_key" } ``` ## Resume a stopped protein sequence redesign run `$ boltz-api protein:sequence-redesign resume` **post** `/compute/v1/protein/sequence-redesign/{id}/resume` Resume a stopped protein sequence redesign run from its last checkpoint ### Parameters - `--id: string` Sequence redesign run ID ### Returns - `ProteinSequenceRedesignResumeResponse: object { id, completed_at, created_at, 14 more }` A fixed-structure protein sequence redesign run. - `id: string` Unique ProteinSequenceRedesignRun identifier - `completed_at: string` - `created_at: string` - `data_deleted_at: string` When the input, output, and result data was permanently deleted. Null if data has not been deleted. - `engine: "boltz-protein-redesign"` Deprecated. Use pipeline instead. - `engine_version: "v2026-07-14"` Deprecated. Use pipeline_version instead. - `error: object { code, message, details }` - `code: string` Machine-readable error code - `message: string` Human-readable error message - `details: optional unknown` Additional field-level error details keyed by input path, when available. - `input: object { entities, num_proteins, structure, 4 more } or object { entities, num_proteins, structure, 4 more }` 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. - `BinderSequenceRedesignTargetEntityResponse: object { chain_id, role, type }` A fixed target chain from the input CIF. - `chain_id: string` - `role: "target"` - `type: "from_template"` - `BinderSequenceRedesignBinderEntityResponse: object { chain_id, role, type, design_motifs }` - `chain_id: string` - `role: "binder"` - `type: "from_template"` - `design_motifs: optional array of object { filters, residues, type }` 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. - `ExcludedAminoAcidsDesignFilterResponse: object { amino_acids, type }` - `amino_acids: array of string` Single-letter amino-acid codes that must not occur in the filtered designed region. - `type: "excluded_amino_acids"` - `MaxHydrophobicFractionDesignFilterResponse: object { max_fraction, type }` - `max_fraction: number` - `type: "max_hydrophobic_fraction"` - `ExcludedSequenceMotifsDesignFilterResponse: object { motifs, type }` - `motifs: array of string` Sequence motifs that must not occur. X matches any single residue. - `type: "excluded_sequence_motifs"` - `residues: array of number` 0-indexed residues to redesign on this chain. - `type: "residues"` - `num_proteins: number` Number of unique filter-passing redesigned proteins to generate. - `structure: object { url, url_expires_at }` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `type: "binder"` - `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. - `ExcludedAminoAcidsDesignFilterResponse: object { amino_acids, type }` - `amino_acids: array of string` Single-letter amino-acid codes that must not occur in the filtered designed region. - `type: "excluded_amino_acids"` - `MaxHydrophobicFractionDesignFilterResponse: object { max_fraction, type }` - `max_fraction: number` - `type: "max_hydrophobic_fraction"` - `ExcludedSequenceMotifsDesignFilterResponse: object { motifs, type }` - `motifs: array of string` Sequence motifs that must not occur. X matches any single residue. - `type: "excluded_sequence_motifs"` - `idempotency_key: optional string` - `workspace_id: optional string` Workspace to run this redesign in. - `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. - `chain_id: string` - `type: "from_template"` - `design_motifs: optional array of object { filters, residues, type }` 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. - `ExcludedAminoAcidsDesignFilterResponse: object { amino_acids, type }` - `amino_acids: array of string` Single-letter amino-acid codes that must not occur in the filtered designed region. - `type: "excluded_amino_acids"` - `MaxHydrophobicFractionDesignFilterResponse: object { max_fraction, type }` - `max_fraction: number` - `type: "max_hydrophobic_fraction"` - `ExcludedSequenceMotifsDesignFilterResponse: object { motifs, type }` - `motifs: array of string` Sequence motifs that must not occur. X matches any single residue. - `type: "excluded_sequence_motifs"` - `residues: array of number` 0-indexed residues to redesign on this chain. - `type: "residues"` - `num_proteins: number` Number of unique filter-passing redesigned proteins to generate. - `structure: object { url, url_expires_at }` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `type: "generic"` - `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. - `ExcludedAminoAcidsDesignFilterResponse: object { amino_acids, type }` - `amino_acids: array of string` Single-letter amino-acid codes that must not occur in the filtered designed region. - `type: "excluded_amino_acids"` - `MaxHydrophobicFractionDesignFilterResponse: object { max_fraction, type }` - `max_fraction: number` - `type: "max_hydrophobic_fraction"` - `ExcludedSequenceMotifsDesignFilterResponse: object { motifs, type }` - `motifs: array of string` Sequence motifs that must not occur. X matches any single residue. - `type: "excluded_sequence_motifs"` - `idempotency_key: optional string` - `workspace_id: optional string` Workspace to run this redesign in. - `livemode: boolean` Whether this resource was created with a live API key. - `pipeline: "boltz-protein-redesign"` - `pipeline_version: "v2026-07-14"` - `progress: object { num_proteins_generated, total_proteins_to_generate, latest_result_id }` - `num_proteins_generated: number` Number of protein binders generated so far - `total_proteins_to_generate: number` Total number of protein binders requested - `latest_result_id: optional string` ID of the most recently generated result - `started_at: string` - `status: "pending" or "running" or "succeeded" or 2 more` - `"pending"` - `"running"` - `"succeeded"` - `"failed"` - `"stopped"` - `stopped_at: string` - `workspace_id: string` Workspace ID - `idempotency_key: optional string` Client-provided idempotency key ### Example ```cli boltz-api protein:sequence-redesign resume \ --api-key 'My API Key' \ --id id ``` #### Response ```json { "id": "id", "completed_at": "2019-12-27T18:11:19.117Z", "created_at": "2019-12-27T18:11:19.117Z", "data_deleted_at": "2019-12-27T18:11:19.117Z", "engine": "boltz-protein-redesign", "engine_version": "v2026-07-14", "error": { "code": "code", "message": "message", "details": {} }, "input": { "entities": [ { "chain_id": "x", "role": "target", "type": "from_template" }, { "chain_id": "x", "role": "target", "type": "from_template" } ], "num_proteins": 1, "structure": { "url": "https://example.com", "url_expires_at": "2019-12-27T18:11:19.117Z" }, "type": "binder", "global_design_filters": [ { "amino_acids": [ "x" ], "type": "excluded_amino_acids" } ], "idempotency_key": "idempotency_key", "workspace_id": "workspace_id" }, "livemode": true, "pipeline": "boltz-protein-redesign", "pipeline_version": "v2026-07-14", "progress": { "num_proteins_generated": 0, "total_proteins_to_generate": 1, "latest_result_id": "latest_result_id" }, "started_at": "2019-12-27T18:11:19.117Z", "status": "pending", "stopped_at": "2019-12-27T18:11:19.117Z", "workspace_id": "workspace_id", "idempotency_key": "idempotency_key" } ``` ## Delete protein sequence redesign run data `$ boltz-api protein:sequence-redesign delete-data` **post** `/compute/v1/protein/sequence-redesign/{id}/delete-data` Permanently delete the input, output, and result data associated with this sequence redesign run. The sequence redesign run record itself is retained with a `data_deleted_at` timestamp. This action is irreversible. ### Parameters - `--id: string` Sequence redesign run ID ### Returns - `ProteinSequenceRedesignDeleteDataResponse: object { id, data_deleted, data_deleted_at }` - `id: string` ID of the resource whose data was deleted - `data_deleted: true` - `data_deleted_at: string` When the data was deleted ### Example ```cli boltz-api protein:sequence-redesign delete-data \ --api-key 'My API Key' \ --id id ``` #### Response ```json { "id": "id", "data_deleted": true, "data_deleted_at": "2019-12-27T18:11:19.117Z" } ``` ## Estimate cost for a protein sequence redesign run `$ boltz-api protein:sequence-redesign estimate-cost` **post** `/compute/v1/protein/sequence-redesign/estimate-cost` Estimate the cost of a protein sequence redesign run without creating any resource or consuming GPU. ### Parameters - `--entity: 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. - `--num-proteins: number` Number of unique filter-passing redesigned proteins to generate. - `--structure: object { type, url } or object { data, media_type, type }` How to provide a CIF structure file. URLs are auto-detected; base64 uploads must use chemical/x-cif media type. - `--type: "binder"` - `--global-design-filter: 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. - `--idempotency-key: optional string` - `--workspace-id: optional string` Workspace to run this redesign in. ### Returns - `ProteinSequenceRedesignEstimateCostResponse: object { breakdown, disclaimer, estimated_cost_usd }` Estimate response with monetary values encoded as decimal strings to preserve precision. - `breakdown: object { application, cost_per_unit_usd, num_units }` Cost breakdown for the billed application. - `application: "structure_and_binding" or "small_molecule_design" or "small_molecule_library_screen" or 4 more` - `"structure_and_binding"` - `"small_molecule_design"` - `"small_molecule_library_screen"` - `"protein_design"` - `"protein_redesign"` - `"protein_library_screen"` - `"adme"` - `cost_per_unit_usd: string` Estimated cost per displayed unit as a decimal string, rounded up to 4 decimal places. This may include token-size multipliers or generation overhead; estimated_cost_usd is the authoritative total. - `num_units: number` Number of billable units in the estimate. The unit depends on the endpoint: samples for structure-and-binding, molecules for ADME, and requested proteins or molecules for design/screen endpoints. - `disclaimer: string` - `estimated_cost_usd: string` Estimated total cost as a decimal string ### Example ```cli boltz-api protein:sequence-redesign estimate-cost \ --api-key 'My API Key' \ --entity '{chain_id: x, role: target, type: from_template}' \ --entity '{chain_id: x, role: target, type: from_template}' \ --num-proteins 1 \ --structure '{type: url, url: https://example.com}' \ --type binder ``` #### Response ```json { "breakdown": { "application": "structure_and_binding", "cost_per_unit_usd": "0.0500", "num_units": 1 }, "disclaimer": "This is an estimate only and may differ from your actual charges. Final billing is based on exact token counts computed at run time. For large library screens, the estimate is extrapolated from a sample and may be less accurate for highly variable inputs.", "estimated_cost_usd": "0.0500" } ```