> ## Documentation Index
> Fetch the complete documentation index at: https://docs.tamarind.bio/llms.txt
> Use this file to discover all available pages before exploring further.

# Tamarind Bio documentation

> Guides for running structure prediction, protein design, and property prediction on Tamarind Bio, from the web app, the API, or an AI assistant.

A sequence is folded into a structure, docked with a small molecule, and scored

New to Tamarind? Start with one of these, or pick a task below.

> [card] [Run your first job](https://docs.tamarind.bio/tasks/structure-prediction.md)
>
> Open the app, pick a tool, and submit a job from your browser.

> [card] [Call the API](https://docs.tamarind.bio/tamarind/api.md)
>
> Submit jobs and fetch results from your own code.

> [card] [Connect an AI assistant](https://docs.tamarind.bio/tamarind/mcp-server.md)
>
> Run Tamarind tools from Claude, ChatGPT, or Cursor over MCP.

## Explore by task

Each task page compares the tools we recommend, what they take and return, and when to use which.

Structure Prediction

Predict 3D structures of proteins, nucleic acids, and complexes.

[Open](https://docs.tamarind.bio/tasks/structure-prediction.md)

Protein Design

Design binders, antibodies, and peptides, or redesign an existing sequence.

[Open](https://docs.tamarind.bio/tasks/protein-design.md)

Property Prediction

Predict stability, solubility, and developability from sequence or structure.

[Open](https://docs.tamarind.bio/tasks/property-prediction.md)

Docking

Place small molecules into protein pockets and rank the poses.

[Open](https://docs.tamarind.bio/tasks/docking.md)

Finetuning

Train a model on your own labeled data, then run it like any other tool.

[Open](https://docs.tamarind.bio/tasks/finetuning.md)

Tool guides

In-depth guides for RFdiffusion, BindCraft, BoltzGen, ProteinMPNN, and more.

[Open](https://docs.tamarind.bio/tools/rfdiffusion.md)

## Build on Tamarind

Run tools at scale, chain them into workflows, and bring your own models.

> [card] [Batch](https://docs.tamarind.bio/tamarind/batch.md)
>
> Run one tool across many inputs and track them as one job.

> [card] [Pipelines](https://docs.tamarind.bio/tamarind/pipelines.md)
>
> Chain tools into a reusable workflow, from target prep to scoring.

> [card] [CLI](https://docs.tamarind.bio/tamarind/cli.md)
>
> Run Tamarind from your terminal, scripts, or AI agents.

> [card] [Custom Tools](https://docs.tamarind.bio/tamarind/custom-tools.md)
>
> Onboard your internal models and run them next to ours.

> [card] [Protein Design Agent](https://docs.tamarind.bio/tamarind/protein-design-agent.md)
>
> Hand off a de novo design campaign that designs, folds, and scores on its own.

> [card] [Scoring](https://docs.tamarind.bio/tamarind/scoring.md)
>
> Score proteins for many properties in one run.

> [card] [Molecules Database](https://docs.tamarind.bio/molecules-database)
>
> Every sequence, structure, and score in your organization, in one place.

> [card] [Model router](https://docs.tamarind.bio/tamarind/model-router.md)
>
> Get a structure prediction tool recommended from FoldBench results.

## Account and administration

[Manage Team
Invite members and manage roles.](https://docs.tamarind.bio/support/manage-team.md)

[Admin Settings
Members, access, integrations, and compute budgets.](https://docs.tamarind.bio/support/admin-settings.md)

[Single Sign-On (SSO)
Connect Okta, Microsoft Entra ID, Google Workspace, or any SAML 2.0 provider.](https://docs.tamarind.bio/support/sso-setup.md)

[Manage Files
Upload, browse, download, and delete files.](https://docs.tamarind.bio/support/manage-files.md)

[S3 Integration
Send job results to your own S3 bucket automatically.](https://docs.tamarind.bio/support/s3-integration.md)

[Compute Hours
How compute hours are counted, and how to read your usage report.](https://docs.tamarind.bio/support/compute-hours.md)

[Data Privacy and Security
Data ownership, IP, storage, and retention, including how the free tier differs.](https://docs.tamarind.bio/support/data-privacy.md)

[Contact support
Email \[info@tamarind.bio\](mailto:info@tamarind.bio) and we'll get back to you.](mailto:info@tamarind.bio)

## More resources

> [card] [API reference](https://app.tamarind.bio/api-docs)
>
> Endpoints, parameters, and schemas for every tool.

> [card] [Changelog](https://changelog.tamarind.bio)
>
> Recent changes to tools, the app, and the platform.


This documentation is built and hosted on [Mintlify](https://mintlify.com), a developer documentation platform.