🧪 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 --setupto 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 |
|---|---|---|
search_papers | Crossref + OpenAlex + S2 | Multi-source paper search with metadata fusion |
get_paper_details | Crossref + OpenAlex + S2 | Full metadata: abstract, authors, citations, references |
find_similar_papers | Semantic Scholar | Content-based paper recommendations |
get_paper_citations | Semantic Scholar | Forward citation graph + context snippets |
get_paper_references | Semantic Scholar | Backward citation graph (bibliography) |
get_author_profile | OpenAlex + S2 | h-index, publications, co-authors, topics |
analyze_research_topic | OpenAlex | Publication volume trends over time |
find_open_access_pdf | Unpaywall | Legal open access PDF URLs |
search_chemrxiv | Crossref + OpenAlex | Chemistry preprint search |
get_chemrxiv_categories | — | List ChemRxiv subject categories |
search_web_of_science | Web of Science | WoS search (requires API key) |
generate_bibtex | Crossref | DOI → BibTeX (single or batch) |
get_journal_metrics | OpenAlex | Impact metrics, open access %, policy |
search_protein_structures | RCSB PDB | Search PDB by keyword, organism, method |
get_protein_structure | 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 |
|---|---|---|
search_compound | PubChem | Name/SMILES/formula → compound data |
get_compound_properties | PubChem | MW, SMILES, InChI, formula, XLogP, TPSA |
profile_compound | Multiple | Comprehensive profile combining several databases |
get_safety_data | PubChem GHS | GHS pictograms, H-statements, P-statements |
translate_compound_ids | UniChem | Convert PubChem ↔ ChEMBL ↔ DrugBank ↔ ChEBI |
search_crystal_structures | COD | Crystallography Open Database search |
search_materials_project | Materials Project | Band gaps, formation energies (requires key) |
search_nist_webbook | NIST | ΔHf, Cp, phase transitions, IR spectra |
search_mass_spectra | MassBank | Mass spectrum search by exact mass or name |
search_binding_data | BindingDB | IC₅₀, Ki, Kd binding affinities |
search_toxicity | EPA CompTox | Toxicity endpoints (requires key) |
classify_natural_product | 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 |
|---|---|---|
predict_retrosynthesis | IBM RXN | Multi-step retrosynthetic analysis |
plan_synthesis | IBM RXN | Forward synthesis route planning |
predict_product | IBM RXN | Predict products from reactants + reagents |
predict_atom_mapping | IBM RXN | Atom-by-atom mapping for mechanisms |
text_to_procedure | IBM RXN | Natural language → structured procedure |
predict_pka | Rowan Science | pKa values (any functional group, aqueous) |
predict_solubility | Rowan Science | Aqueous solubility prediction |
predict_admet | Rowan Science | Absorption, metabolism, toxicity prediction |
search_tautomers | Rowan Science | Enumerate tautomeric forms |
compute_descriptors | Rowan Science | Molecular descriptors from SMILES |
predict_nmr | 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 |
|---|---|---|
peptide_to_smiles | p2smi | Sequence → SMILES (450+ AAs, 5 cyclization types) |
peptide_cyclization_options | p2smi | Which cyclizations does a sequence support? |
generate_peptide_library | p2smi | Random peptide generation with NCAAs, D-stereo |
peptide_properties | p2smi + RDKit | MW, logP, TPSA, HBD/HBA, Lipinski |
check_peptide_synthesis | p2smi | SPPS feasibility: difficult motifs, aggregation |
modify_peptide | p2smi | Apply N-methylation, PEGylation |
calculate_peptide_pi | pichemist | Isoelectric point (8 pKa reference sets) |
calculate_peptide_extinction | pep-calc.com | ε₂₈₀ (Trp/Tyr/Cys contributions) |
get_peptide_ion_series | pep-calc.com | b/y/a/c/z ion ladders for MS/MS |
assign_peptide_ms_peaks | 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 |
|---|---|
calculate_molarity | Solve for any unknown: mass, moles, volume, or MW |
calculate_dilution | C₁V₁ = C₂V₂ with automatic unit handling |
calculate_reaction_mass | Multi-reagent mass calc from equivalents |
calculate_yield | Percent yield from actual / theoretical |
calculate_concentration | M ↔ mM ↔ mg/mL ↔ %w/v ↔ ppm ↔ ppb |
| Tool | Coverage |
|---|---|
lookup_named_reaction | 202 named reactions — conditions, mechanism, scope, limitations |
lookup_rxn_dev_checklist | Structured checklist for reaction development — Kerr et al., Chem. Soc. Rev. 2025 |
lookup_protecting_group | 30 PGs for OH, NH, C=O, COOH with stability / lability matrix |
lookup_workup_procedure | Step-by-step protocols: LAH quench, aqueous extraction, etc. |
lookup_solvent_properties | 32 solvents — bp, density, polarity index, dielectric, miscibility |
lookup_cooling_bath | 24 recipes from −196 °C (lN₂) to +100 °C |
lookup_tlc_stain | 13 stains organized by functional group selectivity |
lookup_column_chromatography | Solvent selection, Rf rules, loading, troubleshooting |
lookup_buffer_recipe | 20+ buffers — PBS, Tris, HEPES, TAE, TBE, RIPA, citrate… |
lookup_amino_acid_properties | 20 canonical AAs — MW, pKa, pI, hydropathy |
lookup_nmr_solvent | 12 solvents — residual ¹H/¹³C shifts, water peak, multiplicity |
lookup_lab_tips | 35 practical tips across 9 categories |
lookup_safety_card | 9 safety cards for hazardous reagents (n-BuLi, NaH, LAH…) |
🔧 Chemistry Utilities — 5 tools
| Tool | What it does |
|---|---|
calculate_isotope_pattern | Isotope distribution from formula/SMILES (Cl, Br, S patterns) |
validate_cas_number | CAS registry check-digit validation |
convert_units | Mass, volume, energy, pressure, temperature, length, amount |
lookup_periodic_table | Z, mass, electron config, electronegativity, radius, group |
calculate_buffer_ph | 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 |
|---|---|---|
format_citation | Crossref | DOI → formatted reference in 20+ styles (ACS, RSC, Nature, Angew, APA…) |
build_bibliography | Crossref | Batch DOIs → numbered, styled reference list |
lookup_iupac_name | PubChem | SMILES → IUPAC systematic name |
name_to_smiles | PubChem | Common name → SMILES + InChI + InChIKey + MW |
format_molecular_formula | Local | C6H12O6 → C₆H₁₂O₆ (Unicode) / \ce{C6H12O6} (LaTeX) / <sub> (HTML) |
lookup_experimental_template | Local | 18 reaction templates with fill-in fields and safety notes |
lookup_journal_guide | Local | Submission requirements for 12 top chemistry journals |
generate_si_checklist | Local | SI checklist tailored to compound type |
lookup_abbreviation | Local | 193 standard abbreviations (solvents, reagents, spectroscopy) |
get_thesis_guide | 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 --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.
| Variable | Service | Free? | What it unlocks |
|---|---|---|---|
RXN_API_KEY | IBM RXN | ✅ | Retrosynthesis, product prediction, atom mapping |
ROWAN_API_KEY | Rowan Science | ✅ | pKa, solubility, ADMET, tautomers, NMR prediction |
SEMANTIC_SCHOLAR_API_KEY | Semantic Scholar | ✅ | Higher rate limits for citations & recommendations |
UNPAYWALL_EMAIL | Unpaywall | ✅ | Open access PDF discovery |
MATERIALS_PROJECT_API_KEY | Materials Project | ✅ | Crystal structures, band gaps, formation energies |
WOS_API_KEY | Web of Science | 🏛️ | Web of Science search (institutional) |
COMPTOX_API_KEY | EPA CompTox | ✅ | 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": "[email protected]"
}
}
}
}
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.