Labmate Mcp

🧪 labmate-mcp

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

[](https://pypi.org/project/labmate-mcp/) [](https://pypi.org/project/labmate-mcp/) [](https://python.org) [](LICENSE)

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

[Quick Start ↓](#-quick-start)   •   [What Can I Do?](#-what-can-i-do-with-this)   •   [All 81 Tools](#-tool-reference)   •   [Configuration](#%EF%B8%8F-configuration)   •   [Examples](#-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.

📚 Literature15 tools ⚗️ Synthesis11 tools 🧪 Bench30 tools 📊 Analysis15 tools ✍️ Publication10 tools

Search papersCitation graphsAuthor profilesPreprintsOpen access PDFs RetrosynthesisForward predictionAtom mappingpKa / ADMETNMR prediction Named reactionsReagent calculatorProtecting groupsSolvent referenceRxn dev checklist Isotope patternsMass spectraBinding dataCrystal structuresSafety data Format citationsBuild bibliographyExperimental templatesJournal guidesSI checklist

🚀 Quick Start

pip install labmate-mcp

Then add this to your Claude config:

Claude Desktop  →  claudedesktopconfig.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.

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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.

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](#%EF%B8%8F-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) / ` (HTML) | | lookupexperimentaltemplate | Local | **18 reaction templates** with fill-in fields and safety notes | | lookupjournalguide | Local | Submission requirements for **12 top chemistry journals** | | generatesichecklist | Local | SI checklist tailored to compound type | | lookupabbreviation | Local | **193 standard abbreviations** (solvents, reagents, spectroscopy) | | getthesis_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.

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](mailto:ccte_api@epa.gov) | ✅ | 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-ro

…

## Source & license

This open-source MCP server is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [JonasRackl](https://github.com/JonasRackl)
- **Source:** [JonasRackl/labmate-mcp](https://github.com/JonasRackl/labmate-mcp)
- **License:** MIT
- **Homepage:** https://github.com/JonasRackl/labmate-mcp#-quick-start

Install and usage instructions live in the source repository linked above.