🧪 labmate-mcp

Your AI lab companion — from literature search to benchwork to publication.

81 tools  ·  25+ scientific APIs  ·  202 named reactions  ·  zero config required

Quick Start ↓   •   What Can I Do?   •   All 81 Tools   •   Configuration   •   Examples

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:

On macOS: ~/Library/Application Support/Claude/claude_desktop_config.json On Windows: %APPDATA%\Claude\claude_desktop_config.json

{
  "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:

"Find the most cited papers on copper-catalyzed C–H activation from the last 5 years"

Searches across multiple databases, ranks by citations, and gives you abstracts and AI-generated summaries.

"Suzuki coupling, 150 mg aryl bromide (MW 261), 5 mol% Pd(PPh₃)₄, 1.3 eq boronic acid, 2.5 eq K₂CO₃ — how much of everything?"

Calculates exact masses for each reagent with your substrate as the limiting reagent.

"I'm developing a new reaction. What should I be thinking about?"

Walks you through a structured reaction development checklist — covering everything from initial mechanistic hypotheses to scope exploration and scale-up.

"I need to protect a primary amine — stable to acid, cleavable by hydrogenation"

Compares protecting groups against a stability matrix and suggests the best match (here: Cbz).

"Format these DOIs as an ACS bibliography, then give me an experimental template for a Buchwald–Hartwig"

Generates a numbered reference list and a fill-in-the-blank procedure with suggested workup and safety notes.

🔧 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.

IBM RXN and Rowan tools require free API keys. See Configuration.

🧬 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.

Aliases: S2_API_KEY, MP_API_KEY, RXN4CHEMISTRY_API_KEY also work.

If you prefer to configure keys manually, add them to your Claude config:

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

Or create ~/.labmate-mcp.env directly:

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.

Alder-Ene · Aldol · Appel · Arbuzov · Arndt-Eistert · Baeyer-Villiger · Balz-Schiemann · Bamford-Stevens · Barton Decarboxylation · Barton-McCombie · Baylis-Hillman · Beckmann · Biginelli · Birch · Bischler-Napieralski · Blanc Chloromethylation · Bouveault-Blanc · Brown Hydroboration · Buchner Ring Expansion · Buchwald-Hartwig (C–N) · Buchwald-Hartwig (C–O) · Burgess Dehydration · Cadiot-Chodkiewicz · Cannizzaro · Carroll · Catellani · CBS · Chan-Lam · Chichibabin · Claisen Condensation · Claisen Rearrangement · Clemmensen · Click (CuAAC) · Comins · Cope Elimination · Cope Rearrangement · Corey-Bakshi-Shibata · Corey-Chaykovsky · Corey-Fuchs · Corey-Kim · Corey-Nicolaou · Corey-Winter · Cross-Metathesis · Curtius · Dakin · Darzens · Dess-Martin · Dieckmann · Diels-Alder · Doering-LaFlamme · Enders SAMP/RAMP · Eschenmoser-Claisen · Eschenmoser-Tanabe Fragmentation · Eschweiler-Clarke · Evans Aldol · Favorskii · Ferrier · Finkelstein · Fischer Esterification · Fischer Indole · Fleming-Tamao · Friedel-Crafts Acylation · Friedel-Crafts Alkylation · Fries · Fukuyama · Gabriel · Gewald · Glaser · Grignard · Grubbs Metathesis · Hantzsch Pyridine · Heck · Henry · Hiyama · Hiyama-Denmark · Hofmann · Horner · Horner-Wadsworth-Emmons · IBX · Ireland-Claisen · Jacobsen Epoxidation · Jones · Julia-Lythgoe · Kharasch · Knoevenagel · Knorr Pyrrole · Koenigs-Knorr · Kolbe · Kulinkovich · Kumada · Lawesson · Lemieux-Johnson · Ley · Liebeskind-Srogl · Lossen · Luche · Malaprade · Mander Methylenation · Mannich · Matteson · Meerwein Arylation · Meerwein Reduction · Meerwein-Ponndorf-Verley · Meinwald · Michael · Midland · Minisci · Mitsunobu · Modified Julia · Mukaiyama Aldol · Myers · Negishi · Noyori · Nozaki-Hiyama-Kishi · Ohira-Bestmann · Olefin Metathesis · Oppenauer · Oppolzer Sultam · Overman · Oxy-Cope · Ozonolysis · Paal-Knorr · Parikh-Doering · Passerini · Paternò-Büchi · Pauson-Khand · Petasis · Peterson · Pfitzner-Moffatt · Piancatelli · Pictet-Spengler · Pinner · Pinnick · Polonovski · Prevost · Prins · Ramberg-Bäcklund · Reductive Amination · Reformatsky · Rieche · Riley · Ring-Closing Metathesis · Ritter · Robinson Annulation · Roskamp · Roush · Rubottom · Saegusa-Ito · Sakurai-Hosomi · Sandmeyer · Schmidt · Shapiro · Sharpless AD · Sharpless AE · Shi Epoxidation · Shiina · Simmons-Smith · Skraup · Sonogashira · Staudinger Ligation · Staudinger Reduction · Steglich · Stetter · Still-Gennari · Stille · Stork Enamine · Strecker · Suzuki · Suzuki-Miyaura · Swern · Takai · Tebbe · TEMPO · Tiffeneau-Demjanov · Transfer Hydrogenation · Trost AAA · Tsuji-Trost · Ugi · Ullmann · Upjohn · Van Leusen · Vilsmeier-Haack · Wacker · Weinreb Amide · Wharton · Williamson · Wittig · Wittig Rearrangement · Wohl-Ziegler · Wolff · Wolff-Kishner · Yamaguchi · Zincke Aldehyde

Based on Kerr, Jenkinson, Sheridan & Sparr, "Reaction Development: A Student's Checklist", Chem. Soc. Rev. 2025, DOI: 10.1039/D4CS01046A. Each section contains guiding questions, specific checks to perform, and practical tips.

🏗️ 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.

📚 Cite

If labmate-mcp is useful in your research, please cite the tools it builds on:

• 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)

Made with 🧪 for chemists who'd rather be in the lab than Googling.