tamarind.bio valid

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.

For agents: Tamarind Bio: computational biology platform with 300+ protein and molecule design tools on managed GPUs, behind a REST job API with an agent skill.

protein designstructure predictionmolecular dockingrest apiagent skill

Their llms.txt

The beginning of the file, from our validated copy saved 2026-10-25T19:11:16.729Z. Cached copy · Source on tamarind.bio

# 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. An agent with no account can mint its own key in one unauthenticated call — see [agent authentication](https://app.tamarind.bio/auth.md).

## 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.
- [Agent authentication](https://app.tamarind.bio/auth.md): How to get a key with no human present — one unauthenticated `POST /api/agent/provision` returns a working key plus a claim link to hand the person you are working for. Read this first if you have no API key.
- [Full REST guide for LLMs](https://app.tamarind.bio/llms-ful
…

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Machine-readable: GET /v1/resolve?q=tamarind.bio · GET /v1/domain/tamarind.bio · this page as Accept: application/json or text/markdown · MCP lookup_domain

Automatically discovered from public files. Inclusion does not imply endorsement or publisher participation.

Claim my listing on Agent Web Map for tamarind.bio:
1. POST https://agentwebmap.com/v1/sites/tamarind.bio/claims and keep claim_id and claim_secret private.
2. Publish the verification line "AgentWebMap verification: <token>" (token from step 1) in https://tamarind.bio/llms.txt, or use the DNS, meta-tag or well-known method the response describes. This only verifies the listing; your website and domain remain yours.
3. POST https://agentwebmap.com/v1/sites/tamarind.bio/verify with {"claim_id": "...", "claim_secret": "..."}.
4. Save the api_key from the answer; it manages the listing (PATCH https://agentwebmap.com/v1/sites/tamarind.bio).
MCP equivalent: tools begin_ownership_claim, then verify_domain, at https://agentwebmap.com/mcp. Docs: https://agentwebmap.com/docs#verify

Corrections or removal requests: contact the directory.