labmate-mcp
Provides access to Web of Science for searching academic literature (requires API key).
Provides access to Semantic Scholar's academic paper database, enabling search, citation graph navigation, author profiles, and suggestion of similar papers.
Click on "Install Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type
@followed by the MCP server name and your instructions, e.g., "@labmate-mcpFind the most cited papers on copper-catalyzed C–H activation from the last 5 years"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
🧪 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-mcpThen 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-mcpRestart Claude. 61 of 81 tools work out of the box — no API keys needed.
Want retrosynthesis, pKa prediction, or NMR shifts? Runlabmate-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.
Ask Claude… | What happens |
"What are the NMR solvent peaks for DMSO-d₆?" | Residual ¹H: 2.50 ppm (quintet), ¹³C: 39.52 ppm, water: 3.33 ppm |
"Generate 20 cyclic pentapeptides with some D-amino acids" | Returns SMILES with MW, logP, and TPSA for each |
"I want to submit to JACS — what do I need to know?" | Word limits, abstract length, citation format, graphical abstract specs |
"Retrosynthesis of ibuprofen" | Multi-step route back to commercial starting materials |
"pKa of 4-nitrophenol?" | Quantum-chemistry prediction via Rowan Science |
"Cooling bath for −42 °C?" | MeCN / dry ice, or chlorobenzene / dry ice |
🔧 Tool Reference
📚 Literature & Discovery — 15 tools
Search papers across multiple databases, explore citation graphs, find open access PDFs, and track research trends.
Tool | Source | What it does |
| Crossref + OpenAlex + S2 | Multi-source paper search with metadata fusion |
| Crossref + OpenAlex + S2 | Full metadata: abstract, authors, citations, references |
| Semantic Scholar | Content-based paper recommendations |
| Semantic Scholar | Forward citation graph + context snippets |
| Semantic Scholar | Backward citation graph (bibliography) |
| OpenAlex + S2 | h-index, publications, co-authors, topics |
| OpenAlex | Publication volume trends over time |
| Unpaywall | Legal open access PDF URLs |
| Crossref + OpenAlex | Chemistry preprint search |
| — | List ChemRxiv subject categories |
| Web of Science | WoS search (requires API key) |
| Crossref | DOI → BibTeX (single or batch) |
| OpenAlex | Impact metrics, open access %, policy |
| RCSB PDB | Search PDB by keyword, organism, method |
| RCSB PDB | Full PDB entry: resolution, ligands, sequence |
🔬 Compound Data & Safety — 12 tools
Look up any compound by name, SMILES, or formula. Get safety data, binding affinities, crystal structures, and more.
Tool | Source | What it does |
| PubChem | Name/SMILES/formula → compound data |
| PubChem | MW, SMILES, InChI, formula, XLogP, TPSA |
| Multiple | Comprehensive profile combining several databases |
| PubChem GHS | GHS pictograms, H-statements, P-statements |
| UniChem | Convert PubChem ↔ ChEMBL ↔ DrugBank ↔ ChEBI |
| COD | Crystallography Open Database search |
| Materials Project | Band gaps, formation energies (requires key) |
| NIST | ΔHf, Cp, phase transitions, IR spectra |
| MassBank | Mass spectrum search by exact mass or name |
| BindingDB | IC₅₀, Ki, Kd binding affinities |
| EPA CompTox | Toxicity endpoints (requires key) |
| GNPS | NP superclass / class / pathway |
⚗️ Computational Chemistry — 11 tools
AI-powered retrosynthesis, forward reaction prediction, pKa, solubility, ADMET, and NMR shift prediction.
Tool | Source | What it does |
| IBM RXN | Multi-step retrosynthetic analysis |
| IBM RXN | Forward synthesis route planning |
| IBM RXN | Predict products from reactants + reagents |
| IBM RXN | Atom-by-atom mapping for mechanisms |
| IBM RXN | Natural language → structured procedure |
| Rowan Science | pKa values (any functional group, aqueous) |
| Rowan Science | Aqueous solubility prediction |
| Rowan Science | Absorption, metabolism, toxicity prediction |
| Rowan Science | Enumerate tautomeric forms |
| Rowan Science | Molecular descriptors from SMILES |
| Rowan Science | ¹H and ¹³C chemical 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.
Tool | Source | What it does |
| p2smi | Sequence → SMILES (450+ AAs, 5 cyclization types) |
| p2smi | Which cyclizations does a sequence support? |
| p2smi | Random peptide generation with NCAAs, D-stereo |
| p2smi + RDKit | MW, logP, TPSA, HBD/HBA, Lipinski |
| p2smi | SPPS feasibility: difficult motifs, aggregation |
| p2smi | Apply N-methylation, PEGylation |
| pichemist | Isoelectric point (8 pKa reference sets) |
| pep-calc.com | ε₂₈₀ (Trp/Tyr/Cys contributions) |
| pep-calc.com | b/y/a/c/z ion ladders for MS/MS |
| pep-calc.com | Match m/z values to fragments |
🧪 Bench Chemistry — 18 tools
Everyday lab calculators and a reference library covering named reactions, protecting groups, solvents, workup protocols, and more.
Tool | What it does |
| Solve for any unknown: mass, moles, volume, or MW |
| C₁V₁ = C₂V₂ with automatic unit handling |
| Multi-reagent mass calc from equivalents |
| Percent yield from actual / theoretical |
| M ↔ mM ↔ mg/mL ↔ %w/v ↔ ppm ↔ ppb |
Tool | Coverage |
| 202 named reactions — conditions, mechanism, scope, limitations |
| Structured checklist for reaction development — |
| 30 PGs for OH, NH, C=O, COOH with stability / lability matrix |
| Step-by-step protocols: LAH quench, aqueous extraction, etc. |
| 32 solvents — bp, density, polarity index, dielectric, miscibility |
| 24 recipes from −196 °C (lN₂) to +100 °C |
| 13 stains organized by functional group selectivity |
| Solvent selection, Rf rules, loading, troubleshooting |
| 20+ buffers — PBS, Tris, HEPES, TAE, TBE, RIPA, citrate… |
| 20 canonical AAs — MW, pKa, pI, hydropathy |
| 12 solvents — residual ¹H/¹³C shifts, water peak, multiplicity |
| 35 practical tips across 9 categories |
| 9 safety cards for hazardous reagents (n-BuLi, NaH, LAH…) |
🔧 Chemistry Utilities — 5 tools
Tool | What it does |
| Isotope distribution from formula/SMILES (Cl, Br, S patterns) |
| CAS registry check-digit validation |
| Mass, volume, energy, pressure, temperature, length, amount |
| Z, mass, electron config, electronegativity, radius, group |
| Henderson-Hasselbalch solver with built-in pKa database |
✍️ Writing & Publication — 10 tools
Format citations, build bibliographies, generate experimental section templates, check journal requirements, and prepare your SI — all from within Claude.
Tool | Source | What it does |
| Crossref | DOI → formatted reference in 20+ styles (ACS, RSC, Nature, Angew, APA…) |
| Crossref | Batch DOIs → numbered, styled reference list |
| PubChem | SMILES → IUPAC systematic name |
| PubChem | Common name → SMILES + InChI + InChIKey + MW |
| Local | C6H12O6 → C₆H₁₂O₆ (Unicode) / |
| Local | 18 reaction templates with fill-in fields and safety notes |
| Local | Submission requirements for 12 top chemistry journals |
| Local | SI checklist tailored to compound type |
| Local | 193 standard abbreviations (solvents, reagents, spectroscopy) |
| Local | Section-by-section writing guide: abstract → SI |
📖 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 --setupThis 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.
Variable | Service | Free? | What it unlocks |
| ✅ | Retrosynthesis, product prediction, atom mapping | |
| ✅ | pKa, solubility, ADMET, tautomers, NMR prediction | |
| ✅ | Higher rate limits for citations & recommendations | |
| ✅ | Open access PDF discovery | |
| ✅ | Crystal structures, band gaps, formation energies | |
| 🏛️ | Web of Science search (institutional) | |
| ✅ | Toxicity & environmental data |
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.
Database | Entries | What's inside | |
⚗️ | Named reactions | 202 | Conditions, mechanism type, scope, limitations |
📋 | Rxn dev checklist | 30 questions | Kinetics, mechanism, DoE, catalysis, scope, scale-up |
🛡️ | Protecting groups | 30 | OH / NH / C=O / COOH, stability matrix |
🧴 | Solvents | 32 | bp, density, polarity index, dielectric, miscibility |
❄️ | Cooling baths | 24 | Recipes from −196 °C to +100 °C |
🎨 | TLC stains | 13 | Selectivity by functional group, recipe, procedure |
🧫 | Buffer recipes | 20+ | Preparation at specific pH, temperature correction |
🧬 | Amino acids | 20 | pKa, pI, MW, hydropathy, special notes |
📻 | NMR solvents | 12 | Residual ¹H, ¹³C, water peak, multiplicity |
📝 | Experimental templates | 18 | Fill-in-the-blank for common reaction types |
📰 | Journal guides | 12 | JACS, Angew, Nature Chem, JOC, Org Lett… |
🔤 | Abbreviations | 193 | Standard abbreviations across 7 categories |
💡 | Lab tips | 35 | Practical tips in 9 categories |
☣️ | Safety cards | 9 | Hazardous reagent protocols |
📄 | SI requirements | 18 | Per-technique formatting and common mistakes |
🎓 | Thesis writing | 6 | Section-by-section guidance |
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.
Section | Questions |
🔍 Take Stock | 5 |
📈 Kinetics & Thermodynamics | 6 |
⚙️ Mechanism | 4 |
📊 Optimisation | 3 |
🔄 Catalysis | 4 |
🎯 Scope | 3 |
🚀 Applications | 5 |
Total | 30 |
🏗️ 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.
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