Labmate MCP

81 chemistry tools — literature, calculations, retrosynthesis

Quick Install

Automated & IDE Setup

Copy the AI prompt to install this server into Claude Code, Cursor, or another agent — or use 1-click editor setup below.

Add to Cursor Add to VS Code

Not yet automatically verified

We haven't yet run this listing's install command through our automated sandbox check. This isn't a red flag — we're steadily working through the catalog.

Manual Client & Custom JSON ConfigExpand JSON ▾

Client Config & Setup

Choose your client or environment

Target File:~/Library/Application Support/Claude/claude_desktop_config.json

claude_desktop_config.json

{
  "mcpServers": {
    "labmate-mcp": {
      "command": "uvx",
      "args": [
        "labmate-mcp"
      ]
    }
  }
}

💡 Paste the JSON block into your client's configuration file under mcpServers, then restart the application.

Documentation Overview

🧪 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

Terminal

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

config.json

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

Claude Code → .mcp.json in your project root

config.json

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

Docker

Terminal

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

Read the full README →View source on GitHub →

Related MCP Servers

View all in Developer Tools View all alternatives

Adoption & maintenance

Factual signals from GitHub, npm, and our automated checks — not a rating.

GitHub stars

Stargazers on the source repository.

Last commit

7mo ago

Most recent push to the default branch.

Directory activity

1 views

Config copies, upvotes, and views on AllMCPs.

Reviews

No reviews yet — be the first to share how this listing worked for you.

Frequently Asked Questions about Labmate MCP

Add the following block to your claude_desktop_config.json under mcpServers: "mcpServers": { "labmate-mcp": { "command": "uvx", "args": ["labmate-mcp"] } }

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Technical Specs & Signals

CategoryDeveloper Tools

11/12 checks healthy over the last 45d

35Quality signal: Fair · 35/100How this signal is calculated ▾

Server availabilityNot measured

Not scored for repo-hosted servers — we can't reach the running server, only its GitHub page. Hosted MCP endpoints are health-checked live.

Verified ownership10/20

Documentation & tools15/30

Adoption & activity1/15

Community engagement0/10

A guidance signal from public completeness & health data — not a user rating. New listings start lower and rise as they add docs, get verified, and grow adoption. Signals we can't observe for a listing are skipped, not counted against it.

Supply-chain signal

No high-severity advisories surfaced by our automated scan.

Critical 0High 0Medium 0Low 0

Scanned 5d ago via OSV.dev · labmate-mcp (PyPI)

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More in 💻 Developer Tools →Best MCP servers for Developers →Alternatives to Labmate MCP →Install in Claude Desktop Install in Cursor Install in VS Code Setup guides for all 13 MCP clients

Labmate MCP

81 chemistry tools — literature, calculations, retrosynthesis

Quick Install

Automated & IDE Setup

Copy the AI prompt to install this server into Claude Code, Cursor, or another agent — or use 1-click editor setup below.

Add to Cursor Add to VS Code

Not yet automatically verified

We haven't yet run this listing's install command through our automated sandbox check. This isn't a red flag — we're steadily working through the catalog.

Manual Client & Custom JSON ConfigExpand JSON ▾

Client Config & Setup

Choose your client or environment

Target File:~/Library/Application Support/Claude/claude_desktop_config.json

claude_desktop_config.json

{
  "mcpServers": {
    "labmate-mcp": {
      "command": "uvx",
      "args": [
        "labmate-mcp"
      ]
    }
  }
}

💡 Paste the JSON block into your client's configuration file under mcpServers, then restart the application.

Documentation Overview

🧪 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

Terminal

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

config.json

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

Claude Code → .mcp.json in your project root

config.json

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

Docker

Terminal

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

Read the full README →View source on GitHub →

Related MCP Servers

View all in Developer Tools View all alternatives

Adoption & maintenance

Factual signals from GitHub, npm, and our automated checks — not a rating.

GitHub stars

Stargazers on the source repository.

Last commit

7mo ago

Most recent push to the default branch.

Directory activity

1 views

Config copies, upvotes, and views on AllMCPs.

Reviews

No reviews yet — be the first to share how this listing worked for you.

Frequently Asked Questions about Labmate MCP

Add the following block to your claude_desktop_config.json under mcpServers: "mcpServers": { "labmate-mcp": { "command": "uvx", "args": ["labmate-mcp"] } }

AllMCPs Directory Badge

Full Badge Customizer

Showcase your server listing on GitHub or your project documentation. Embed this dynamic SVG badge to highlight official listing status and live engagement.

Badge Style:

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Markdown (GitHub README)

[![AllMCPs](https://allmcps.com/api/badge/labmate-mcp?style=directory)](https://allmcps.com/mcp/labmate-mcp)

HTML Embed

<a href="https://allmcps.com/mcp/labmate-mcp"><img src="https://allmcps.com/api/badge/labmate-mcp?style=directory" alt="Labmate MCP on AllMCPs" /></a>

Technical Specs & Signals

CategoryDeveloper Tools

11/12 checks healthy over the last 45d

35Quality signal: Fair · 35/100How this signal is calculated ▾

Server availabilityNot measured

Not scored for repo-hosted servers — we can't reach the running server, only its GitHub page. Hosted MCP endpoints are health-checked live.

Verified ownership10/20

Documentation & tools15/30

Adoption & activity1/15

Community engagement0/10

Supply-chain signal

No high-severity advisories surfaced by our automated scan.

Critical 0High 0Medium 0Low 0

Scanned 5d ago via OSV.dev · labmate-mcp (PyPI)

★ Spotlight Slot

Feature Your MCP Server

Get maximum visibility for your server across our directory, search results, and detail pages.

Spotlight Your Server

Own this project?

Free dofollow backlink: add your website and place the AllMCPs badge on it — no claim needed. We detect it automatically and keep it verified as long as the badge stays live.

Claim & get free dofollow

Share & Embed

Add our SVG badge (dark/light directory styles) or embeddable widget to your site.

Explore more

More in 💻 Developer Tools →Best MCP servers for Developers →Alternatives to Labmate MCP →Install in Claude Desktop Install in Cursor Install in VS Code Setup guides for all 13 MCP clients