Labmate MCP

Name: Labmate MCP
Author: JonasRackl

by JonasRacklversion 7.3.1i★ –iRuns on your computer

Registry nameio.github.JonasRackl/labmate-mcp

Install

Overview

Description from the maker (original English)

81 chemistry tools — literature, calculations, retrosynthesis

PopNx MCP’s three pillars

These three are never merged into one score: opinions, measurements and popularity are different things.

User voiceiNo reviews yetReviews open together with accounts in a later step
Our basic checksi1 of 1 passedChecked from public information; code not scanned yet
UsageiNot measured yet★ –

What you can do with it

We have not written a plain-language summary for this one yet. Below are the facts we read from the registry.

Connection: Runs on your computer
Transport: stdio
Category: Other
You need to fill in: RXN_API_KEY, ROWAN_API_KEY

Install

Pick the AI app you use, then copy the settings.

Before you install

Basic checks: 1 of 1 passed
Runs on your computer with your user’s permissions (files, network, apps).
You fill in yourself: RXN_API_KEY, ROWAN_API_KEY

Values marked secret are keys to your account. Never share them or paste them into a chat.

You need

PyPIPython’s uv installed (for the uvx command)

Which app do you use?

ClaudeClaude CodeCursorVS CodeChatGPT

Pick your app above. We remember it, so next time the button says “Install in …”.

Open Claude Desktop → Settings → Developer → Edit Config, and paste this into claude_desktop_config.json

{
  "mcpServers": {
    "labmate": {
      "command": "uvx",
      "args": [
        "labmate-mcp"
      ],
      "env": {
        "RXN_API_KEY": "your-value",
        "ROWAN_API_KEY": "your-value"
      }
    }
  }
}

Run this in your terminal

claude mcp add labmate --env RXN_API_KEY=your-value --env ROWAN_API_KEY=your-value -- uvx labmate-mcp

Fill in the empty values before running it.

Open in Cursor

Or copy the settings yourself

Paste into .cursor/mcp.json in your project, or ~/.cursor/mcp.json

{
  "mcpServers": {
    "labmate": {
      "command": "uvx",
      "args": [
        "labmate-mcp"
      ],
      "env": {
        "RXN_API_KEY": "your-value",
        "ROWAN_API_KEY": "your-value"
      }
    }
  }
}

Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.

Open in VS Code

Or copy the settings yourself

Paste into .vscode/mcp.json in your project

{
  "servers": {
    "labmate": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "labmate-mcp"
      ],
      "env": {
        "RXN_API_KEY": "your-value",
        "ROWAN_API_KEY": "your-value"
      }
    }
  }
}

Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.

This one runs on your computer, and ChatGPT can only connect to servers on the internet. Pick another app.

Your choice stays on this device in a cookie; no account needed.

Values you fill in

RXN_API_KEY secret env
IBM RXN key for retrosynthesis (free)
ROWAN_API_KEY secret env
Rowan key for pKa/NMR predictions (free)

These settings are generated from the maker’s registry entry. If the README says otherwise, follow the README.

What it can do

Runs on your computer; the tool list appears in your AI app after you install it.

Basic checksi

We check information anyone can see; we have not read the code. Checks that do not apply are left out of the count. · Checked Nov 7, 2026

✓ Pass
Maker matches the repo
The registry name was verified with the GitHub account JonasRackl, which owns the repo
… Not checked yet
Still maintained
We have not read this repo from GitHub yet
… Not checked yet
Has a licence
We have not read this repo from GitHub yet
– Not applicable
Endpoint responds
This one runs on your computer; there is no internet endpoint
– Not applicable
Sign-in with OAuth
Runs on your computer and uses local settings instead
… Not checked yet
No hidden instructions in tool descriptions
Runs on your computer; we can only read tool lists from internet endpoints

Compared with others in Otheri

More stars than 0% of the other 32688 servers in this category
Published to the registry more recently than 2% of the other 32688 servers in this category
Basic checks equal to or better than 100% of the other 32688 servers in this category

Compared with every active server in this category in the registry. Stars count only when the publisher owns the repo.

Common questions

Is Labmate MCP safe?

It passed 1 of 1 applicable basic checks. We have not read the code. Before adding a key or token, see what access the server asks for and use a key with only the permissions you need.

What keys or codes does it need?

You need to fill in: RXN_API_KEY, ROWAN_API_KEY

Does it run on my computer or in the cloud?

It runs on your computer. Your AI app starts it when needed, and data does not pass through the maker’s servers (unless it calls an online service itself).

Is it still maintained?

The GitHub repo last changed –, and the latest version (7.3.1) reached the registry 9 months ago.

Which apps can use it?

Apps that support MCP, such as Claude Desktop, Claude Code, Cursor and VS Code. You also need Python (uv) on your computer.

What can I use instead?

In the same category: Spec Driven Development, Remote Desktop Commander, 御府和田玉在售作品查询

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README from the maker

Open the README

Copied from the maker’s repo as written. PopNx MCP has not reviewed or endorsed it. HTML, images and scripts are removed. Links lead off this site.

🧪 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

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.

💬 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

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…

| `looku

Only the beginning is shown; read the rest in the repo

Labmate MCP

Overview

PopNx MCP’s three pillars

What you can do with it

Install

Before you install

Values you fill in

What it can do

Basic checksi

Maker matches the repo

Still maintained

Has a licence

Endpoint responds

Sign-in with OAuth

No hidden instructions in tool descriptions

Compared with others in Otheri

Common questions

Alternatives

Spec Driven Development

Remote Desktop Commander

御府和田玉 在售作品查询

README from the maker

🧪 labmate-mcp

🚀 Quick Start

💬 What Can I Do With This?

🔧 Tool Reference

📚 Literature & Discovery — 15 tools

🔬 Compound Data & Safety — 12 tools

⚗️ Computational Chemistry — 11 tools

🧬 Peptide Chemistry — 10 tools

🧪 Bench Chemistry — 18 tools

御府和田玉在售作品查询