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io.github.JonasRackl/labmate-mcp

81 chemistry tools — literature, calculations, retrosynthesis

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🧪 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.

📚 Literature 15 tools	⚗️ Synthesis 11 tools	🧪 Bench 30 tools	📊 Analysis 15 tools	✍️ Publication 10 tools
Search papers Citation graphs Author profiles Preprints Open access PDFs	Retrosynthesis Forward prediction Atom mapping pKa / ADMET NMR prediction	Named reactions Reagent calculator Protecting groups Solvent reference Rxn dev checklist	Isotope patterns Mass spectra Binding data Crystal structures Safety data	Format citations Build bibliography Experimental templates Journal guides SI checklist

🚀 Quick Start

pip install labmate-mcp

Then add this to your Claude config:

Claude Desktop → claude_desktop_config.json

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

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

Claude Code → .mcp.json in your project root

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

Docker

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.

More things you can ask

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.

Show all 15 tools

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.

Show all 12 tools

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.

Show all 11 tools

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.

Show all 10 tools

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.

Show all 5 calculators

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

Show all 13 reference tools

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

Show all 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.

Show all 10 tools

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.

Available API keys

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.

Manual configuration

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

All 202 named reactions

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

Reaction development checklist — 7 sections

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.