# Tamarind Bio

> Computational biology platform: hundreds of tools for protein structure prediction, protein/antibody/peptide/binder design, docking, binding affinity, MSA generation and molecular dynamics, all behind one uniform REST job API. A hosted MCP server is also available.

The links below are root-relative, against **`https://app.tamarind.bio`**.

## Start here

- [Homepage as Markdown](/index.md): What the platform is, what you can run, and a step-by-step setup runbook for an agent to follow. The HTML homepage redirects into the signed-in app and carries nothing readable, so this is the entry point if you arrived at the root URL.
- [Agent skill](/SKILL.md): Self-contained SKILL.md for AI agents — install the CLI, get an API key, find the right tool, validate, submit, download, plus the contract rules that break generated code. Start here if you are an agent about to write code; it is task-shaped and short.
- [Full API guide for LLMs](/llms-full.txt): The complete REST reference — auth, tool discovery, submit/poll/download, file-handling rules, and every contract detail. Longer and reference-shaped; read it when the skill is not enough.
- [Tool catalog, no API key required](/tools.json): Every publicly submittable `type` value, each with a description, intent tags (`antibody-design`, `binder-design`, `protein-ligand-docking`, `structure-prediction`, …) and its REQUIRED settings — enough to build a correct payload before you have a key. Narrow it with `?type=` or `?tag=` instead of pulling the whole file. Generated live from the tool registry, so it is never stale. Also available as [tools.md](/tools.md). Absence is not proof a name is invalid: feature-flagged, org-restricted and custom tools are omitted here but may be submittable with your key — check `GET /api/tools` once you have one.

## Reference

- [OpenAPI specification](/api/openapi.json): OpenAPI spec for the job/file API merged with the live pipelines and molecules surfaces. It FAILS SOFT: if the backend spec cannot be fetched, the response is still a 200 carrying the classic surface alone, with the pipelines and molecules paths silently absent — so if you generate a client from it, check that the paths you need are present rather than concluding they do not exist.
- [Per-tool settings schema](/api/tools/alphafold/schema): `GET /api/tools/{type}/schema` returns one tool's full parameters — use it instead of downloading the whole spec. Requires `x-api-key`; without one it answers 400. The keyless catalog above carries only each tool's REQUIRED settings.
- [MCP server](https://mcp.tamarind.bio/mcp): Hosted Model Context Protocol server (streamable HTTP; OAuth 2.1 or `x-api-key`). Prefer this over raw HTTP when your client supports MCP. Setup guide: https://docs.tamarind.bio/tamarind/mcp-server
- [Interactive API docs](/api-docs): Browser UI for exploring endpoints and building a payload. Human-oriented; agents should read llms-full.txt instead.
- [Product documentation](https://docs.tamarind.bio): Guides, tool notes, and task-level tool recommendations. Every page is also available as Markdown by appending `.md`.

## Notes for agents

- Tool names are exact and case-sensitive. The human display name is not a valid `type` (`AlphaFold` is a label; `alphafold` is the type).
- Never send a `type` or a settings key you did not read from `GET /api/tools`, `/tools.json`, or a tool's schema endpoint — an unrecognised key is NOT rejected and NOT removed — it is flagged internally and carried through — so a synonym never satisfies the field it was meant to be, and the submit fails as "missing required field" without telling you the key was wrong.
- Every REST route lives under `/api/` — `POST /api/submit-job`, `GET /api/jobs`, `POST /api/result`. There is no rewrite from the bare path, so `POST /submit-job` is a 404.
- `POST /api/validate-job` dry-runs a payload without spending a job. Use it before every submit. It still needs `x-api-key` — free of compute, not free of auth — and answers 400 without one, so it is not a step you can take from the keyless catalog above.
- A missing or incorrect API key returns HTTP **401** on `/api/jobs`. Classic submit, result, file, tool, and validation endpoints answer **400** instead; `/api/models`, `/api/finetuned-models`, and `/api/usage-statistics` also answer **401**. Branch on "not 2xx", not on a specific code.
- There is no official SDK. The PyPI package `tamarind` and the npm package `tamarind` are unrelated third-party projects — do not install them.