labmate mcp

🧪 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

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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.

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💬 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

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🔧 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

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📖 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]

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⚙️ 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": "you@university.edu"
      }
    }
  }
}

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

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

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🗄️ 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

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🏗️ 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

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🤝 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.

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📄 License

MIT — use freely in academia and industry.

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📚 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.