> ## Documentation Index > Fetch the complete documentation index at: https://docs.revilico.bio/llms.txt > Use this file to discover all available pages before exploring further. # Start a AlphaFold run > Predicts a protein's 3D structure from its amino-acid sequence with AlphaFold 2 (ColabFold): one or more proteins predicted separately, or several chains folded together as a complex. Returns five ranked models per prediction with confidence scores. Alignments of related proteins, and templates from the PDB when asked for, are found inside Revilico. Starts a run and returns it with status `queued`; poll GET /v1/runs/{runId} until it finishes. Runs spend credits. **Limits:** `maxSequences`: 20, `minResiduesPerSequence`: 16, `maxResiduesPerPrediction`: 1500, `modelsPerSeed`: 5. How the engine works and how to read its results: [AlphaFold documentation](/docs/alphafold-openfold). **Scope:** `runs:write`. ## OpenAPI ````yaml /api-reference/openapi.json post /v1/engines/alphafold/runs openapi: 3.1.0 info: title: Revilico API version: 1.0.0 description: >- Run Revilico's computational chemistry and biology engines from your own code: upload input files, start runs, follow them and read their results. servers: - url: https://public-api.revilico.bio security: - bearerAuth: [] tags: - name: Account description: Who you are, your credits and what your runs have used. - name: Engines description: The engines you can run, their parameter schemas and examples. - name: Files description: 'Upload input files: create an upload, then PUT the bytes.' - name: Runs description: Start, follow and cancel engine runs. - name: Results and outputs description: 'Read what a run produced: results, files and outputs.' - name: Projects description: Group runs into the projects you see in the web app. - name: Sharing description: >- Share runs with people in your organization, as in the web app's Pipeline sharing. - name: Notes description: >- RevNotes: read, write and share the rich-text notes and note folders of the web app's RevNotes panel, in markdown or HTML. - name: Drive description: >- Your RevDrive files and shared drives, as in the web app: browse, read, use files as run inputs, save outputs, and organize. Ids: `dfile_…` and `dfld_…` in a personal Drive, `drive_…` for a shared drive, `sdfile_…` and `sdfld_…` in one. - name: Engine runs description: >- Start a run of one engine, with that engine's parameters and input files. Same endpoint as **Start a run**. - name: Health description: Service status. Needs no API key. paths: /v1/engines/alphafold/runs: post: tags: - Engine runs summary: Start a AlphaFold run description: >- Predicts a protein's 3D structure from its amino-acid sequence with AlphaFold 2 (ColabFold): one or more proteins predicted separately, or several chains folded together as a complex. Returns five ranked models per prediction with confidence scores. Alignments of related proteins, and templates from the PDB when asked for, are found inside Revilico. Starts a run and returns it with status `queued`; poll GET /v1/runs/{runId} until it finishes. Runs spend credits. **Limits:** `maxSequences`: 20, `minResiduesPerSequence`: 16, `maxResiduesPerPrediction`: 1500, `modelsPerSeed`: 5. How the engine works and how to read its results: [AlphaFold documentation](/docs/alphafold-openfold). **Scope:** `runs:write`. operationId: engineRuns.alphafold requestBody: required: true content: application/json: schema: type: object properties: name: description: A name for the run, shown in the web app. type: string maxLength: 200 parameters: type: object properties: sequences: minItems: 1 maxItems: 20 type: array items: type: string minLength: 16 maxLength: 1500 pattern: ^[ACDEFGHIKLMNPQRSTVWYX]+$ description: >- One protein chain in one-letter amino-acid codes (ACDEFGHIKLMNPQRSTVWYX; X for unknown), 16–1500 residues. description: >- The protein chains to predict, 1–20. Each is predicted on its own unless complex is true. complex: default: false description: >- Fold all the sequences together as one complex of chains that bind each other (a dimer, say; repeat a sequence for each copy). False predicts each sequence separately. Only matters with 2+ sequences. A complex may have at most 1500 residues in total. type: boolean alignment: default: local description: >- Whether to build an alignment of related proteins first, which usually makes predictions of natural proteins much more accurate. "local" (default) searches UniRef30 inside Revilico; if that search fails, the run fails. The first run on a fresh machine spends about 8 minutes copying the search databases. "none" uses the sequence alone: faster, but confidence for natural proteins is often low. type: string enum: - local - none templates: default: none description: >- Whether to guide the prediction with solved structures of similar proteins. "pdb" searches a copy of the Protein Data Bank (PDB) kept inside Revilico and uses the closest matches; if none match, the run predicts without them. It helps most when the alignment finds few related proteins, or with alignment "none". "none" (default) uses no templates. type: string enum: - none - pdb relax_top_models: default: 5 description: >- How many of the 5 ranked models to clean up with a short physics-based relaxation (fixes clashes and bond geometry). 0 skips it, which is faster. type: number enum: - 0 - 1 - 5 relax_max_iterations: default: 200 description: Relaxation steps per model; 0 runs until it converges. type: number enum: - 0 - 200 - 2000 model_type: default: auto description: >- Model weights. "auto" (default) uses alphafold2_multimer_v3 when complex is true and alphafold2_ptm otherwise. alphafold2_ptm suits single chains; the alphafold2_multimer versions are trained on complexes (v3 is the newest). type: string enum: - auto - alphafold2_ptm - alphafold2_multimer_v1 - alphafold2_multimer_v2 - alphafold2_multimer_v3 - deepfold_v1 num_recycles: default: 3 description: >- Refinement passes per model. More can help hard targets and take longer. auto: 20 for multimer models, 3 otherwise. anyOf: - type: string const: auto - type: number enum: - 0 - 1 - 3 - 6 - 12 - 24 - 48 recycle_early_stop_tolerance: default: auto description: >- Stop recycling once the structure moves less than this (Å) between passes. auto: 0.5 for multimer models, off otherwise. anyOf: - type: string const: auto - type: number enum: - 0 - 0.5 - 1 num_seeds: default: 1 description: >- Random seeds per model. Each seed adds 5 models to rank, and run time grows in step. type: number enum: - 1 - 2 - 4 - 8 - 16 use_dropout: default: false description: >- Sample the model with dropout on, for more varied models. Usually combined with several seeds. type: boolean required: - sequences additionalProperties: false inputs: type: object properties: {} additionalProperties: false budget: description: Most credits the run may spend; it is stopped beyond that. type: number exclusiveMinimum: 0 projectId: description: >- Add the run to this project (`proj_…`); needs editor or owner on it. type: string required: - parameters additionalProperties: false examples: defaults: summary: >- Predict one protein, with an alignment of related proteins built inside Revilico. value: name: Ubiquitin structure parameters: sequences: - >- MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG inputs: {} separate-proteins: summary: >- Predict two unrelated proteins in one run, each on its own, relaxing only the best model of each. value: name: Ubiquitin and CDK2 fragment parameters: sequences: - >- MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG - >- MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASA relax_top_models: 1 inputs: {} sequence-only: summary: >- Predict from the sequence alone, without an alignment: faster, less accurate for natural proteins. value: name: Ubiquitin, sequence only parameters: sequences: - >- MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG alignment: none inputs: {} pdb-templates: summary: >- Guide the prediction with solved structures of similar proteins from the PDB, found inside Revilico. value: name: Ubiquitin with PDB templates parameters: sequences: - >- MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG templates: pdb inputs: {} homodimer: summary: >- Fold two copies of a chain together as a complex; the default model type picks the multimer model. value: name: Ubiquitin dimer parameters: sequences: - >- MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG - >- MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG complex: true inputs: {} responses: '202': description: OK content: application/json: schema: $ref: '#/components/schemas/Run' '400': $ref: '#/components/responses/400' '401': $ref: '#/components/responses/401' '402': $ref: '#/components/responses/402' '403': $ref: '#/components/responses/403' '404': $ref: '#/components/responses/404' '422': $ref: '#/components/responses/422' '500': $ref: '#/components/responses/500' '502': $ref: '#/components/responses/502' components: schemas: Run: type: object properties: id: type: string description: Run id, `run_…`. engine: type: string description: Engine slug, e.g. `revredox`. name: type: - string - 'null' access: type: string enum: - owner - shared - project description: >- Why you can see the run: you started it, it was shared with you, or it is in a project you belong to. Only the owner can cancel it or read its inputs. owner: type: object properties: name: type: - string - 'null' email: type: string required: - name - email description: Who started the run. status: type: string enum: - queued - running - succeeded - failed - cancelled description: >- queued until the engine picks the run up; succeeded, failed and cancelled are final. statusReason: description: >- Why a cancelled run stopped: `user`, `insufficient_credits` or `budget_exceeded`. Null otherwise. type: - string - 'null' progress: type: number description: Progress the engine reports; 0 until it reports any. createdAt: type: string format: date-time startedAt: anyOf: - type: string format: date-time - type: 'null' endedAt: anyOf: - type: string format: date-time - type: 'null' budget: description: Most credits the run may spend, if one was set. type: - number - 'null' creditsUsed: type: number description: Credits charged to the run so far. error: anyOf: - type: object properties: message: type: string required: - message - type: 'null' description: Set when status is failed. children: type: object properties: total: type: number queued: type: number running: type: number succeeded: type: number failed: type: number cancelled: type: number required: - total - queued - running - succeeded - failed - cancelled description: >- For engines that run each input as its own job: how many children are in each status. GET /v1/runs/{runId}/children lists them. links: type: object propertyNames: type: string additionalProperties: type: string description: >- Related endpoints: self, inputs (owner only), results, outputs, files. warnings: description: >- Set when the run was created but a follow-up step, such as adding it to a project, failed. type: array items: type: string required: - id - engine - name - access - owner - status - statusReason - progress - createdAt - startedAt - endedAt - budget - creditsUsed - error - links Error: type: object properties: error: type: object properties: code: type: string enum: - VALIDATION_FAILED - INVALID_ID - INVALID_PARAMETERS - INPUT_LIMIT_EXCEEDED - NOT_FOUND - FORBIDDEN - METHOD_NOT_ALLOWED - CONFLICT - PAYLOAD_TOO_LARGE - MISSING_CREDENTIALS - INVALID_CREDENTIALS - WRONG_ENVIRONMENT - CREDENTIALS_EXPIRED - CREDENTIALS_REVOKED - ACCOUNT_INACTIVE - API_ACCESS_NOT_ENABLED - INSUFFICIENT_SCOPE - SESSION_REQUIRED - TOO_MANY_AUTH_FAILURES - API_KEY_LIMIT_REACHED - ENGINE_NOT_ENABLED - DOCS_NOT_AVAILABLE - INSUFFICIENT_CREDITS - RUN_NOT_COMPLETE - ENGINE_SUBMIT_FAILED - RATE_LIMITED - SERVICE_UNAVAILABLE - INTERNAL_ERROR description: Stable within /v1; branch on this, not on the message. message: type: string description: Readable explanation, for people. details: description: >- Extra context, e.g. `issues` ({ path, message }[]) for validation errors. type: object propertyNames: type: string additionalProperties: {} required: - code - message required: - error responses: '400': description: >- The request is malformed. `error.code` is one of `VALIDATION_FAILED`, `INVALID_ID`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: VALIDATION_FAILED message: The request is malformed. '401': description: >- The API key is missing or not valid. `error.code` is one of `MISSING_CREDENTIALS`, `INVALID_CREDENTIALS`, `WRONG_ENVIRONMENT`, `CREDENTIALS_EXPIRED`, `CREDENTIALS_REVOKED`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: MISSING_CREDENTIALS message: The API key is missing or not valid. '402': description: >- Your organization doesn't have enough credits. `error.code` is one of `INSUFFICIENT_CREDITS`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: INSUFFICIENT_CREDITS message: Your organization doesn't have enough credits. '403': description: >- The key may not do this. `error.code` is one of `INSUFFICIENT_SCOPE`, `API_ACCESS_NOT_ENABLED`, `ENGINE_NOT_ENABLED`, `ACCOUNT_INACTIVE`, `FORBIDDEN`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: INSUFFICIENT_SCOPE message: The key may not do this. '404': description: Not found, or not visible to you. `error.code` is one of `NOT_FOUND`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: NOT_FOUND message: Not found, or not visible to you. '422': description: >- The parameters or input files don't fit the engine. `error.code` is one of `INVALID_PARAMETERS`, `INPUT_LIMIT_EXCEEDED`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: INVALID_PARAMETERS message: The parameters or input files don't fit the engine. '500': description: >- Something went wrong on our side. `error.code` is one of `INTERNAL_ERROR`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: INTERNAL_ERROR message: Something went wrong on our side. '502': description: >- The engine service rejected or failed the request. `error.code` is one of `ENGINE_SUBMIT_FAILED`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: ENGINE_SUBMIT_FAILED message: The engine service rejected or failed the request. securitySchemes: bearerAuth: type: http scheme: bearer description: >- An API key from the web app (**Settings → Developer**), sent as `Authorization: Bearer rvl_live_…`. ```` This documentation is built and hosted on [Mintlify](https://mintlify.com), a developer documentation platform.