labmate-mcp is an MCP server that connects Claude to scientific databases, computational chemistry tools, bench references, and writing utilities. One install covers the entire research workflow.

🚀 Quick Start

pip install labmate-mcp

Then add this to your Claude config:

{
  "mcpServers": {
    "labmate": {
      "command": "labmate-mcp"
    }
  }
}

{
  "mcpServers": {
    "labmate": {
      "command": "labmate-mcp"
    }
  }
}

docker build -t labmate-mcp .
docker run -it labmate-mcp

Restart Claude. 61 of 81 tools work out of the box — no API keys needed.

[!TIP] Want retrosynthesis, pKa prediction, or NMR shifts? Run labmate-mcp --setup to add free API keys.

💬 What Can I Do With This?

Just talk to Claude naturally:

🔧 Tool Reference

📚 Literature & Discovery — 15 tools

Search papers across multiple databases, explore citation graphs, find open access PDFs, and track research trends.

🔬 Compound Data & Safety — 12 tools

Look up any compound by name, SMILES, or formula. Get safety data, binding affinities, crystal structures, and more.

⚗️ Computational Chemistry — 11 tools

AI-powered retrosynthesis, forward reaction prediction, pKa, solubility, ADMET, and NMR shift prediction.

🧬 Peptide Chemistry — 10 tools

Sequence-to-SMILES conversion with 450+ amino acids, cyclization, library generation, pI calculation, and MS/MS interpretation.

🧪 Bench Chemistry — 18 tools

Everyday lab calculators and a reference library covering named reactions, protecting groups, solvents, workup protocols, and more.

🔧 Chemistry Utilities — 5 tools

✍️ Writing & Publication — 10 tools

Format citations, build bibliographies, generate experimental section templates, check journal requirements, and prepare your SI — all from within Claude.

📖 Examples

Literature workflow

You:    "Find the 5 most cited papers on photoredox catalysis from 2020–2024"
Claude: [returns papers ranked by citations with abstracts and TLDRs]

You:    "Who cited paper #2? What topics did they focus on?"
Claude: [shows forward citation graph with context snippets]

You:    "Is there a free PDF for paper #3?"
Claude: [finds a legal open access link via Unpaywall]

You:    "Generate BibTeX for all 5"
Claude: [outputs formatted BibTeX entries]

Synthesis planning

You:    "I want to make 4-methoxybiphenyl from 4-bromoanisole"
Claude: [suggests Suzuki coupling, gives conditions and literature precedent]

You:    "Calculate amounts for a 200 mg scale, 5 mol% catalyst"
Claude: [returns exact mg for every reagent and solvent volume]

You:    "What's a good workup?"
Claude: [aqueous workup protocol with solvent, drying agent, and column conditions]

Reaction development

You:    "I have a new C–H activation — how do I figure out the mechanism?"
Claude: [suggests KIE, radical clocks, Hammett, Stern–Volmer, and computational approaches]

You:    "Walk me through optimisation"
Claude: [covers DoE vs one-variable-at-a-time, green metrics, solvent screening]

You:    "How do I prove this is catalytic, not stoichiometric?"
Claude: [mercury drop test, hot filtration, TON benchmarks, nonlinear effects]

Writing a paper

You:    "Format these 12 DOIs as an ACS bibliography"
Claude: [numbered reference list in ACS style]

You:    "Give me an experimental template for a Sonogashira"
Claude: [fill-in-the-blank procedure with safety notes]

You:    "What SI do I need for a small molecule paper?"
Claude: [checklist with ¹H/¹³C NMR, HRMS, mp, HPLC, formatting tips]

You:    "I'm submitting to Angew — what are the requirements?"
Claude: [word limits, abstract format, citation style, graphical abstract specs]

⚙️ Configuration

The easiest way to add API keys:

labmate-mcp --setup

This walks you through each key and saves them to ~/.labmate-mcp.env. They're loaded automatically whenever you use labmate.

All keys are optional. 61 of 81 tools work without any configuration.

{
  "mcpServers": {
    "labmate": {
      "command": "labmate-mcp",
      "env": {
        "RXN_API_KEY": "your-rxn-key",
        "ROWAN_API_KEY": "your-rowan-key",
        "UNPAYWALL_EMAIL": "you@university.edu"
      }
    }
  }
}

RXN_API_KEY=your-rxn-key
ROWAN_API_KEY=your-rowan-key

🗄️ Built-in Databases

Everything below ships with labmate — no API calls, no internet required.

🏗️ Architecture

labmate_mcp/
├── server.py       5,248 lines   81 MCP tool definitions + response formatting
├── bench.py        4,714 lines   Calculators + reference databases
├── apis.py         1,744 lines   HTTP clients for 25+ scientific APIs
├── writing.py      1,488 lines   Citations, templates, journal guides, SI, thesis
├── chemistry.py      572 lines   Isotope patterns, CAS, units, periodic table, pH
├── peptide.py        384 lines   p2smi + pichemist + pep-calc.com integration
└── __init__.py         4 lines   Version
                  ──────────────
                  14,154 lines

🤝 Contributing

Contributions are welcome! See CONTRIBUTING.md for details.

High-impact areas: more named reactions, more experimental templates, more journal guides, tests, and bug reports.

📄 License

MIT — use freely in academia and industry.

• Reaction development checklist — Kerr, M. A.; Jenkinson, M. A.; Sheridan, H.; Sparr, C. Chem. Soc. Rev. 2025. doi:10.1039/D4CS01046A
• p2smi — Feller, A. JOSS 2025, 10, 8319. doi:10.21105/joss.08319
• pichemist — Trastoy, B. et al. J. Chem. Inf. Model. 2023. AstraZeneca/peptide-tools
• OpenAlex — Priem, J.; Piwowar, H.; Orr, R. arXiv:2205.01833 (2022)