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.

📚 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.

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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

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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.

Show all 15 tools

🔬 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

⚗️ Computational Chemistry — 11 tools

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

Show all 11 tools

*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

🧪 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

Show all 13 reference tools

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