Labmate

Labmate MCP Server integrates Claude with a comprehensive set of scientific data sources, computation tools, bench references, and writing utilities to streamline every stage of your research workflow from literature search to publication. This MCP server provides an all-in-one setup that you can run locally or in a container to empower Claude to perform complex, chemistry-focused tasks with minimal setup.

How to use

You interact with the Labmate MCP Server through a compatible MCP client that connects to the server either locally or over HTTP. Start the server using the command shown in your chosen setup method, then configure your client to point at the server. Once connected, you can ask Claude to search literature, plan syntheses, run bench calculations, analyze data, and format publications all within a single conversational flow.

How to install

Prerequisites: you need Python installed on your system. You may also choose to run the server inside Docker for isolation and ease of deployment.

Step 1: Install the package using Python’s package manager.

Step 2: Run the server or use the provided setup commands to initialize API keys and environment configuration.

Step 3: Connect your MCP client by configuring the server endpoint and start the client. The setup flow includes optional API keys for extended capabilities.

Configuration and usage notes

The server supports configuration through a simple, explicit setup flow. You can start with an automatic setup that saves credentials to a local environment file, or you can provide credentials manually in your client’s configuration. The available API keys cover a range of services, but all keys are optional and 61 of 81 tools work without any configuration.

If you want to run the server in Docker, you can build a container image and start the container to run Labmate MCP Server in an isolated environment.

Examples of what you can do with Labmate MCP Server

Literature and discovery: search papers across multiple sources, view abstracts, access open PDFs, and generate BibTeX for a selected set.

Synthesis planning: perform retrosynthesis or forward planning, compute exact reagent masses for a scale, and obtain workup suggestions.

Reaction development and bench references: consult named reactions, apply a reaction development checklist, and pull protecting group and solvent references.

Writing and publication: format citations, build bibliographies, generate experimental templates, and assemble SI checklists.

Troubleshooting and tips

If you encounter connectivity issues, verify that your MCP client is configured to connect to the Labmate MCP Server endpoint and that the server is running. For workflow tips, use the setup command to obtain free API keys for extended capabilities and consult the example prompts to guide your conversations.

Available tools

search_papers

Multi-source literature search across Crossref, OpenAlex, and S2 with metadata fusion

get_paper_details

Retrieve full metadata for a paper including abstract, authors, citations, and references

find_similar_papers

Content-based recommendations for related literature from Semantic Scholar

get_paper_citations

Forward citation graph with context snippets for a given paper

get_paper_references

Backward citation graph (bibliography) for a paper

get_author_profile

Author profile with h-index, publications, co-authors, and topics from multiple sources

analyze_research_topic

Publication volume trends over time for a given topic using OpenAlex data

find_open_access_pdf

Open access PDFs discovery via Unpaywall

search_chemrxiv

ChemRxiv preprint search across Crossref and OpenAlex

get_chemrxiv_categories

List of ChemRxiv subject categories

search_web_of_science

WoS search (requires API key)

generate_bibtex

DOI to BibTeX conversion for single or batch DOIs

get_journal_metrics

OpenAlex-based journal metrics and open access data

search_protein_structures

RCSB PDB search by keyword, organism, or method

get_protein_structure

Full PDB entry details including resolution and ligands