labmate-mcp

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🧪 labmate-mcp

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

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81 tools &nbsp;·&nbsp; 25+ scientific APIs &nbsp;·&nbsp; 202 named reactions &nbsp;·&nbsp; zero config required

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Quick Start ↓ &nbsp;&nbsp;•&nbsp;&nbsp; What Can I Do? &nbsp;&nbsp;•&nbsp;&nbsp; All 81 Tools &nbsp;&nbsp;•&nbsp;&nbsp; Configuration &nbsp;&nbsp;•&nbsp;&nbsp; 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.

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<table> <tr> <td align="center" width="20%"><b>📚 Literature</b><br>15 tools</td> <td align="center" width="20%"><b>⚗️ Synthesis</b><br>11 tools</td> <td align="center" width="20%"><b>🧪 Bench</b><br>30 tools</td> <td align="center" width="20%"><b>📊 Analysis</b><br>15 tools</td> <td align="center" width="20%"><b>✍️ Publication</b><br>10 tools</td> </tr> <tr> <td align="center">Search papers<br>Citation graphs<br>Author profiles<br>Preprints<br>Open access PDFs</td> <td align="center">Retrosynthesis<br>Forward prediction<br>Atom mapping<br>pKa / ADMET<br>NMR prediction</td> <td align="center">Named reactions<br>Reagent calculator<br>Protecting groups<br>Solvent reference<br>Rxn dev checklist</td> <td align="center">Isotope patterns<br>Mass spectra<br>Binding data<br>Crystal structures<br>Safety data</td> <td align="center">Format citations<br>Build bibliography<br>Experimental templates<br>Journal guides<br>SI checklist</td> </tr> </table>

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🚀 Quick Start

pip install labmate-mcp

Then add this to your Claude config:

<details> <summary><b>Claude Desktop</b> &nbsp;→&nbsp; <code>claude_desktop_config.json</code></summary>

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

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

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<details> <summary><b>Claude Code</b> &nbsp;→&nbsp; <code>.mcp.json</code> in your project root</summary>

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

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<details> <summary><b>Docker</b></summary>

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docker build -t labmate-mcp .
docker run -it labmate-mcp

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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:

<table> <tr><td>

"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.

</td></tr> <tr><td>

"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.

</td></tr> <tr><td>

"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.

</td></tr> <tr><td>

"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).

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"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.

</td></tr> </table>

<details> <summary><b>More things you can ask</b></summary>

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| 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.

<details> <summary>Show all 15 tools</summary>

| 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 |

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🔬 Compound Data & Safety — 12 tools

Look up any compound by name, SMILES, or formula. Get safety data, binding affinities, crystal structures, and more.

<details> <summary>Show all 12 tools</summary>

| 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 |

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⚗️ Computational Chemistry — 11 tools

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

<details> <summary>Show all 11 tools</summary>

| 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.

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🧬 Peptide Chemistry — 10 tools

Sequence-to-SMILES conversion with 450+ amino acids, cyclization, library generation, pI calculation, and MS/MS interpretation.

<details> <summary>Show all 10 tools</summary>

| 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 |

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🧪 Bench Chemistry — 18 tools

Everyday lab calculators and a reference library covering named reactions, protecting groups, solvents, workup protocols, and more.

<details> <summary>Show all 5 calculators</summary>

| 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 |

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<details> <summary>Show all 13 reference tools</summary>

| 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…) |

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🔧 Chemistry Utilities — 5 tools

<details> <summary>Show all 5 tools</summary>

| 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 |

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✍️ Writing & Publication — 10 tools

Format citations, build bibliographies, generate experimental section templates, check journal requirements, and prepare your SI — all from within Claude.

<details> <summary>Show all 10 tools</summary>

| 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.

<details> <summary><b>Available API keys</b></summary>

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| 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.

</details>

<details> <summary><b>Manual configuration</b></summary>

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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

</details>

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🗄️ Built-in Databases

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

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| | 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 |

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<details> <summary><b>All 202 named reactions</b></summary>

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

</details>

<details> <summary><b>Reaction development checklist — 7 sections</b></summary>

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 |

</details>

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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:

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• 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)

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

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