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Tamarind Bio Molecular Tools

Run cloud protein structure, design, docking and binding tools via the Tamarind Bio API

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
5 files

What it does

Once installed, the agent knows how to use the Tamarind Bio cloud platform to run open-source molecular and structural biology tools (such as AlphaFold, Boltz, RFdiffusion, ProteinMPNN, DiffDock and Vina) without needing a local GPU. It can look up available tools, check job settings, submit jobs with an API key, poll for completion and download results. Note that the agent still needs a Tamarind account and API key, and results should be checked scientifically by the user.

Great for

  • Researchers who want to run protein structure prediction or docking in the cloud without local GPUs
  • Computational biology teams submitting batches of sequences for structural or biophysical characterization
  • Developers building pipelines that call the Tamarind REST API or MCP server

Skip it if

  • Users without a Tamarind Bio account or API key, since the skill cannot run jobs without credentials
  • Local-only sequence processing or molecular descriptor work, which the skill itself says should use a local library instead; uploading sensitive or unpublished sequences to a third-party cloud also carries data-confidentiality risk
  • Anyone relying on outputs for clinical or safety decisions without expert validation, since the skill states it does not establish scientific accuracy for any model

Try asking

  • “Predict the 3D structure of this protein sequence using AlphaFold or Boltz on Tamarind”
  • “Dock this ligand against my target protein with DiffDock and summarise the top poses”
  • “Design nanobody binders for this antigen using BoltzGen via Tamarind”
  • “Check which Tamarind tools are available for binding-affinity prediction”
Step-by-step guide: how to use Tamarind Bio Molecular ToolsInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 5 original files, the MIT licence and an attribution note.

    tamarind.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip tamarind.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip tamarind.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Fetch the account's current schema for each tool before submitting, and use the normalized settings returned by validation
  • Check your Tamarind allowance and compute budget before scaling up to large batches, since free usage is not guaranteed indefinitely
  • Keep your API key in the environment variable rather than in files or logs, and verify scientific outputs yourself after download

What's inside

  • references/api_reference.md
  • references/examples.md
  • references/tool_catalog.md
  • references/workflows.md
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.