Labmate Mcp

io.github.JonasRacklPublished by GitHub account JonasRacklv7.3.1Updated Oct 27, 2026

81 chemistry tools — literature, calculations, retrosynthesis

VerifiedSTDIODesktop onlyWeb Search & ScrapingKnowledge & MemoryAI & ML

Overview

AI-generated overview

A chemistry research MCP server with 81 tools covering literature search, compound data, retrosynthesis, bench calculators and citation formatting.

What you can do
  • Search papers across Crossref, OpenAlex and Semantic Scholar, follow citation graphs, find author profiles, preprints and open access PDFs
  • Look up compounds, properties, safety data, crystal structures, spectra, binding affinities and protein structures
  • Run computational chemistry: retrosynthesis, product prediction, atom mapping, pKa, solubility, ADMET and NMR shift prediction
  • Convert peptide sequences to SMILES, generate libraries, check synthesis feasibility and interpret MS/MS ions
  • Use bench calculators and reference lookups for molarity, reaction mass, named reactions, protecting groups, solvents, workup, stains, buffers and safety cards
  • Format citations and bibliographies, build…
When to use it
Useful for chemists and students who want an assistant to help with literature review, synthesis planning, reaction development, lab calculations and manuscript preparation in one place. Most reference and calculator tools work without any configuration.
Requirements
Runs locally as a Python package installed with pip, launched over stdio from the Claude Desktop or Claude Code configuration. Optional free API keys enable extra tools: ROWAN_API_KEY for pKa, solubility, ADMET and NMR prediction, and RXN_API_KEY for retrosynthesis and product prediction; further optional keys cover Semantic Scholar, Unpaywall, Materials Project, Web of Science and EPA CompTox. Keys can be saved to a local env file or set in the server config.
Before you install
Several tools send queries to third-party scientific APIs, so search terms and structures leave the machine. Optional keys such as ROWAN_API_KEY, RXN_API_KEY, WOS_API_KEY and COMPTOX_API_KEY are stored in a local env file or config; protect that file. Predicted pKa, ADMET, NMR and retrosynthesis results are model estimates and should not replace experimental verification or safety assessment.

Installation

In SourceWeft

  1. Open Labmate Mcp in the dashboard and add it to a workspace.
  2. Enable the server for the chats that should use its tools.

Desktop only via STDIO. STDIO servers start a local process, so they need the SourceWeft desktop host.

Other MCP clients

Follow the launch instructions in the repository.

README


🧪 labmate-mcp

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


[PyPI version] [Downloads] [Python] [License]


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

bash
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

json
{  "mcpServers": {    "labmate": {      "command": "labmate-mcp"    }  }}
Claude Code  →  .mcp.json in your project root
json
{  "mcpServers": {    "labmate": {      "command": "labmate-mcp"    }  }}
Docker
bash
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
ToolSourceWhat it does
search_papersCrossref + OpenAlex + S2Multi-source paper search with metadata fusion
get_paper_detailsCrossref + OpenAlex + S2Full metadata: abstract, authors, citations, references
find_similar_papersSemantic ScholarContent-based paper recommendations
get_paper_citationsSemantic ScholarForward citation graph + context snippets
get_paper_referencesSemantic ScholarBackward citation graph (bibliography)
get_author_profileOpenAlex + S2h-index, publications, co-authors, topics
analyze_research_topicOpenAlexPublication volume trends over time
find_open_access_pdfUnpaywallLegal open access PDF URLs
search_chemrxivCrossref + OpenAlexChemistry preprint search
get_chemrxiv_categories—List ChemRxiv subject categories
search_web_of_scienceWeb of ScienceWoS search (requires API key)
generate_bibtexCrossrefDOI → BibTeX (single or batch)
get_journal_metricsOpenAlexImpact metrics, open access %, policy
search_protein_structuresRCSB PDBSearch PDB by keyword, organism, method
get_protein_structureRCSB PDBFull 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
ToolSourceWhat it does
search_compoundPubChemName/SMILES/formula → compound data
get_compound_propertiesPubChemMW, SMILES, InChI, formula, XLogP, TPSA
profile_compoundMultipleComprehensive profile combining several databases
get_safety_dataPubChem GHSGHS pictograms, H-statements, P-statements
translate_compound_idsUniChemConvert PubChem ↔ ChEMBL ↔ DrugBank ↔ ChEBI
search_crystal_structuresCODCrystallography Open Database search
search_materials_projectMaterials ProjectBand gaps, formation energies (requires key)
search_nist_webbookNISTΔHf, Cp, phase transitions, IR spectra
search_mass_spectraMassBankMass spectrum search by exact mass or name
search_binding_dataBindingDBIC₅₀, Ki, Kd binding affinities
search_toxicityEPA CompToxToxicity endpoints (requires key)
classify_natural_productGNPSNP superclass / class / pathway

⚗️ Computational Chemistry — 11 tools

AI-powered retrosynthesis, forward reaction prediction, pKa, solubility, ADMET, and NMR shift prediction.

Show all 11 tools
ToolSourceWhat it does
predict_retrosynthesisIBM RXNMulti-step retrosynthetic analysis
plan_synthesisIBM RXNForward synthesis route planning
predict_productIBM RXNPredict products from reactants + reagents
predict_atom_mappingIBM RXNAtom-by-atom mapping for mechanisms
text_to_procedureIBM RXNNatural language → structured procedure
predict_pkaRowan SciencepKa values (any functional group, aqueous)
predict_solubilityRowan ScienceAqueous solubility prediction
predict_admetRowan ScienceAbsorption, metabolism, toxicity prediction
search_tautomersRowan ScienceEnumerate tautomeric forms
compute_descriptorsRowan ScienceMolecular descriptors from SMILES
predict_nmrRowan Science¹H 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
ToolSourceWhat it does
peptide_to_smilesp2smiSequence → SMILES (450+ AAs, 5 cyclization types)
peptide_cyclization_optionsp2smiWhich cyclizations does a sequence support?
generate_peptide_libraryp2smiRandom peptide generation with NCAAs, D-stereo
peptide_propertiesp2smi + RDKitMW, logP, TPSA, HBD/HBA, Lipinski
check_peptide_synthesisp2smiSPPS feasibility: difficult motifs, aggregation
modify_peptidep2smiApply N-methylation, PEGylation
calculate_peptide_pipichemistIsoelectric point (8 pKa reference sets)
calculate_peptide_extinctionpep-calc.comε₂₈₀ (Trp/Tyr/Cys contributions)
get_peptide_ion_seriespep-calc.comb/y/a/c/z ion ladders for MS/MS
assign_peptide_ms_peakspep-calc.comMatch 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
ToolWhat it does
calculate_molaritySolve for any unknown: mass, moles, volume, or MW
calculate_dilutionC₁V₁ = C₂V₂ with automatic unit handling
calculate_reaction_massMulti-reagent mass calc from equivalents
calculate_yieldPercent yield from actual / theoretical
calculate_concentrationM ↔ mM ↔ mg/mL ↔ %w/v ↔ ppm ↔ ppb
Show all 13 reference tools
ToolCoverage
lookup_named_reaction202 named reactions — conditions, mechanism, scope, limitations
lookup_rxn_dev_checklistStructured checklist for reaction development — Kerr et al., Chem. Soc. Rev. 2025
lookup_protecting_group30 PGs for OH, NH, C=O, COOH with stability / lability matrix
lookup_workup_procedureStep-by-step protocols: LAH quench, aqueous extraction, etc.
lookup_solvent_properties32 solvents — bp, density, polarity index, dielectric, miscibility
lookup_cooling_bath24 recipes from −196 °C (lN₂) to +100 °C
lookup_tlc_stain13 stains organized by functional group selectivity
lookup_column_chromatographySolvent selection, Rf rules, loading, troubleshooting
lookup_buffer_recipe20+ buffers — PBS, Tris, HEPES, TAE, TBE, RIPA, citrate…
lookup_amino_acid_properties20 canonical AAs — MW, pKa, pI, hydropathy
lookup_nmr_solvent12 solvents — residual ¹H/¹³C shifts, water peak, multiplicity
lookup_lab_tips35 practical tips across 9 categories
lookup_safety_card9 safety cards for hazardous reagents (n-BuLi, NaH, LAH…)

🔧 Chemistry Utilities — 5 tools

Show all 5 tools
ToolWhat it does
calculate_isotope_patternIsotope distribution from formula/SMILES (Cl, Br, S patterns)
validate_cas_numberCAS registry check-digit validation
convert_unitsMass, volume, energy, pressure, temperature, length, amount
lookup_periodic_tableZ, mass, electron config, electronegativity, radius, group
calculate_buffer_phHenderson-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
ToolSourceWhat it does
format_citationCrossrefDOI → formatted reference in 20+ styles (ACS, RSC, Nature, Angew, APA…)
build_bibliographyCrossrefBatch DOIs → numbered, styled reference list
lookup_iupac_namePubChemSMILES → IUPAC systematic name
name_to_smilesPubChemCommon name → SMILES + InChI + InChIKey + MW
format_molecular_formulaLocalC6H12O6 → C₆H₁₂O₆ (Unicode) / \ce{C6H12O6} (LaTeX) / <sub> (HTML)
lookup_experimental_templateLocal18 reaction templates with fill-in fields and safety notes
lookup_journal_guideLocalSubmission requirements for 12 top chemistry journals
generate_si_checklistLocalSI checklist tailored to compound type
lookup_abbreviationLocal193 standard abbreviations (solvents, reagents, spectroscopy)
get_thesis_guideLocalSection-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:

bash
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
VariableServiceFree?What it unlocks
RXN_API_KEYIBM RXN✅Retrosynthesis, product prediction, atom mapping
ROWAN_API_KEYRowan Science✅pKa, solubility, ADMET, tautomers, NMR prediction
SEMANTIC_SCHOLAR_API_KEYSemantic Scholar✅Higher rate limits for citations & recommendations
UNPAYWALL_EMAILUnpaywall✅Open access PDF discovery
MATERIALS_PROJECT_API_KEYMaterials Project✅Crystal structures, band gaps, formation energies
WOS_API_KEYWeb of Science🏛️Web of Science search (institutional)
COMPTOX_API_KEYEPA 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:

json
{  "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:

bash
RXN_API_KEY=your-rxn-keyROWAN_API_KEY=your-rowan-key

🗄️ Built-in Databases

Everything below ships with labmate — no API calls, no internet required.

DatabaseEntriesWhat's inside
⚗️Named reactions202Conditions, mechanism type, scope, limitations
📋Rxn dev checklist30 questionsKinetics, mechanism, DoE, catalysis, scope, scale-up
🛡️Protecting groups30OH / NH / C=O / COOH, stability matrix
🧴Solvents32bp, density, polarity index, dielectric, miscibility
❄️Cooling baths24Recipes from −196 °C to +100 °C
🎨TLC stains13Selectivity by functional group, recipe, procedure
🧫Buffer recipes20+Preparation at specific pH, temperature correction
🧬Amino acids20pKa, pI, MW, hydropathy, special notes
📻NMR solvents12Residual ¹H, ¹³C, water peak, multiplicity
📝Experimental templates18Fill-in-the-blank for common reaction types
📰Journal guides12JACS, Angew, Nature Chem, JOC, Org Lett…
🔤Abbreviations193Standard abbreviations across 7 categories
💡Lab tips35Practical tips in 9 categories
☣️Safety cards9Hazardous reagent protocols
📄SI requirements18Per-technique formatting and common mistakes
🎓Thesis writing6Section-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.

SectionQuestions
🔍 Take Stock5
📈 Kinetics & Thermodynamics6
⚙️ Mechanism4
📊 Optimisation3
🔄 Catalysis4
🎯 Scope3
🚀 Applications5
Total30

🏗️ 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:


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


Source: README.md at commit 4530400

Tools

0
SourceWeft has not started this package in its sandbox yet, so its tools are not known.

Version history

1
  1. v7.3.1LatestSep 16, 2026

Score

50% of the applicable checks met

How complete this listing is, computed from the registry entry, the endpoint and public sources. Not a rating of the server and not a statement that it is safe or working today: reachability is a dated check, and no installs or reviews go into the score.

  • Reached in the last 30 days25 pts

    Keep the endpoint answering the MCP handshake; SourceWeft probes it every 30 days.

  • Auth declared10 pts

    Declare the credential headers in the registry entry, or keep the endpoint answering the probe so its auth can be classified.

  • Tools listed15 pts

    Answer tools/list without a credential, or ship a package that starts in a sandbox without one.

  • DescriptionRequired15 pts
  • Logo10 pts
  • Documentation15 pts
  • License10 pts