# Tamarind Bio

> Tamarind Bio is a computational biology platform for protein and molecule design. 300+ published state-of-the-art tools — structure prediction, antibody and binder design, inverse folding, docking, binding affinity, MSA generation, molecular dynamics — run on managed GPUs behind one uniform REST job API. No local GPU, no installation, no parameterization.

Tamarind runs the methods research teams actually cite — AlphaFold, Boltz, RFdiffusion, ProteinMPNN, BindCraft, GROMACS and hundreds more — without the high-performance computing, dependency management, and command-line work they normally require. Biologists and chemists use the web app; agents, scripts and pipelines use the same tools through the REST API, the CLI, or the hosted MCP server. Every tool is one `type` string against one endpoint, so adding a new method to a pipeline does not mean learning a new interface.

AI agents can start with the [Agent skill](https://app.tamarind.bio/SKILL.md), then discover the live tool catalog at https://app.tamarind.bio/tools.json — no API key required.

## What you can run

- **Structure prediction** — fold a sequence, predict a complex, model a protein–ligand system (AlphaFold, Boltz, Chai-1, ESMFold)
- **Protein and binder design** — de novo binders, scaffolds and motif grafting (RFdiffusion, BindCraft)
- **Antibody and nanobody design** — structure prediction, affinity maturation, humanization, developability (RFantibody, ImmuneBuilder, BioPhi)
- **Inverse folding and sequence design** — sequences for a given backbone, with or without ligands (ProteinMPNN, LigandMPNN)
- **Docking** — protein–ligand and protein–protein, blind or pocket-directed (AutoDock Vina, DiffDock, GNINA)
- **Binding affinity and scoring** — ΔΔG, developability metrics, aggregation and immunogenicity risk
- **Peptides, enzymes and small molecules** — cyclic peptide design, enzyme engineering, ADMET and generative chemistry
- **Molecular dynamics** — GROMACS simulation and analysis

The authoritative, always-current list is the keyless catalog below. Individual tool pages are indexed in [the sitemap](https://www.tamarind.bio/sitemap.xml).

## For AI agents and coding agents

These live on the app host and are written to be read by machines.

- [Agent skill](https://app.tamarind.bio/SKILL.md): Self-contained SKILL.md — install the CLI, get an API key, find the right tool, validate, submit, download, plus the contract rules that most often break generated code. Start here if you are about to write code.
- [Full REST guide for LLMs](https://app.tamarind.bio/llms-full.txt): The complete reference — auth, tool discovery, submit/poll/download, file handling, pipelines and every contract detail. Read it when the skill is not enough.
- [Tool catalog, no API key required](https://app.tamarind.bio/tools.json): Every publicly submittable tool `type` with its description, intent tags and REQUIRED settings — enough to build a correct payload before you have an account. Generated live from the registry, so it cannot go stale. Narrow with `?type=alphafold` or `?tag=protein-ligand-docking` rather than pulling the whole document. Same data as a table: [tools.md](https://app.tamarind.bio/tools.md).
- [Homepage as Markdown](https://app.tamarind.bio/index.md): Platform overview and a step-by-step setup runbook. The app's HTML root redirects into the signed-in shell and has nothing readable in it.
- [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: [/api-docs/mcp-server](https://app.tamarind.bio/api-docs/mcp-server)
- [CLI](https://app.tamarind.bio/api-docs/cli): `uv tool install tamarind-cli` (or `pip install tamarind-cli`). A thin client over the same REST API; emits JSON when stdout is not a TTY, so it works in scripts and CI.
- [Agent capabilities catalog](https://app.tamarind.bio/.well-known/ai-catalog.json): Machine-readable index of everything above.
- [API catalog](https://app.tamarind.bio/.well-known/api-catalog): RFC 9727 machine-readable index of the APIs, including the OpenAPI specification.
- [MCP server card](https://app.tamarind.bio/.well-known/mcp/server-card.json): What the MCP server exposes, for a client deciding whether to connect.

## API

- [OpenAPI specification](https://app.tamarind.bio/api/openapi.json): The job/file API merged with the live pipelines and molecules surfaces.
- [Interactive API docs](https://app.tamarind.bio/api-docs): Browser UI for exploring endpoints and building a payload. Human-oriented; agents should read llms-full.txt instead.
- [Get an API key](https://app.tamarind.bio/api-docs/api-key): Keys and rate limits.
- [Product documentation](https://docs.tamarind.bio): Guides, tool notes and task-level recommendations. Every page is also available as Markdown by appending `.md`.

## Solutions

- [Antibody discovery and engineering](https://www.tamarind.bio/antibody)
- [Enzyme engineering](https://www.tamarind.bio/enzyme)
- [Peptide discovery](https://www.tamarind.bio/peptide)
- [Small molecule discovery](https://www.tamarind.bio/small-molecule)

## Get started

- [Sign up](https://app.tamarind.bio/sign-up) · [Sign in](https://app.tamarind.bio/sign-in) · [Open the app](https://app.tamarind.bio/app)
- [Pricing](https://www.tamarind.bio/pricing)
- [Book a demo](https://calendly.com/founders-cji/tamarind-bio)

## Company

- [Features](https://www.tamarind.bio/features)
- [Blog](https://www.tamarind.bio/blog)
- [Contact](https://www.tamarind.bio/contact)
- [Trust Center](https://trust.tamarind.bio/)
- [Careers](https://www.ycombinator.com/companies/tamarind-bio/jobs)
- [Terms of Service](https://app.tamarind.bio/terms-of-service)

## Notes for agents

- **Installing:** `uv tool install tamarind-cli` (or `pip install tamarind-cli`). There is no Python or JavaScript SDK library — the CLI and the REST API are the two supported paths. The PyPI package `tamarind` and the npm package `tamarind` are unrelated third-party projects, so `pip install tamarind` does not get you this platform.
- Tool names are exact and case-sensitive. The human display name is not a valid `type` (`AlphaFold` is a label; `alphafold` is the type). Confirm a name against `/tools.json` instead of guessing it.
- 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 compute. Use it before every submit. It needs an API key too — free of compute, not free of auth.
- A missing or incorrect API key returns HTTP 400 on the job/file endpoints, not 401. Branch on "not 2xx", not on a specific code.
- Jobs run minutes to hours. Submit and poll asynchronously rather than blocking.