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  • pubchem-mcp-server

    cyanheads
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    maintenance
    Enables AI agents and applications to search, retrieve, and analyze chemical compounds, substances, and bioassays from PubChem's vast chemical information database through comprehensive tools for chemical research and discovery.
    10
    404
    9
    Apache 2.0

  • UniProt MCP Server

    vitamin3615
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    license
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    quality
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    maintenance
    An MCP server that enables language models to fetch protein information from the UniProt database, including protein details, sequences, functions, and structures.
    MIT

  • @cyanheads/uniprot-mcp-server

    cyanheads
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    quality
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    maintenance
    Search UniProtKB by protein function, fetch curated records, map IDs across databases, and pull reference proteomes, taxonomy, and sequences via MCP. Supports both STDIO and Streamable HTTP transports.
    66
    1
    Apache 2.0

  • reactome-mcp

    tc2fh
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    license
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    quality
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    maintenance
    Enables coding agents to interact with the Reactome pathway database, including search, lookup, hierarchy traversal, SBML/SBGN export, and gene-set enrichment analysis.
    17
    MIT

  • pubmed-mcp-server

    cyanheads
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    maintenance
    A bridge connecting AI agents to NCBI's PubMed database through the Model Context Protocol, enabling seamless searching, retrieval, and analysis of biomedical literature and data.
    11
    3,327
    134
    Apache 2.0

  • reactome-db-mcp

    tc2fh
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    quality
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    maintenance
    Provides direct SQL access to a locally hosted Reactome database, enabling schema discovery, guarded read-only queries, and ergonomic helpers over the full relational schema.
    9
    MIT

  • ChemCP

    scottmreed
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    quality
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    maintenance
    Renders interactive 2D molecular structure diagrams from SMILES notation and computes molecular properties like molecular weight, LogP, and TPSA, directly in the chat.
    1
    60
    1
    ISC

  • uniprot-mcp

    fzlzjerry
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    license
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    quality
    B
    maintenance
    MCP server that exposes the UniProt REST API to LLM clients, enabling search and retrieval of protein data via tools like search_uniprotkb, get_entry, and map_ids.
    7
    MIT
  • CEDAR MCP Server by musen-lab

    CEDAR MCP Serverofficial

    musen-lab
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    license
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    quality
    A
    maintenance
    Enables interaction with the CEDAR metadata repository, including fetching templates, searching BioPortal ontology terms, and managing template instances.
    8
    MIT

  • MCP GeneLab Server

    sbl-sdsc
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    quality
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    maintenance
    Converts natural language queries into Cypher queries against the NASA GeneLab Knowledge Graph, enabling AI-assisted analysis of spaceflight experiments and their biological effects.
    12
    3
    BSD 3-Clause

  • kegg-mcp-server

    Lucas-Servi
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    quality
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    maintenance
    An MCP server for querying the KEGG bioinformatics database, providing tools, resource templates, and guided prompts for pathways, genes, compounds, and more.
    34
    3
    MIT

  • mcp-ubergraph-query

    twhetzel
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    license
    A
    quality
    D
    maintenance
    Enables AI assistants to query the Ubergraph biomedical ontology SPARQL endpoint with tools for custom SPARQL queries, term lookup, search, and hierarchy traversal.
    4
    MIT
  • millimap-mcp by milliomics

    millimap-mcpofficial

    milliomics
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    license
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    quality
    D
    maintenance
    Enables Claude Desktop to read and drive analyses on the active MilliMap session, including datasets, clusters, annotations, and markers.
    12
    MIT

  • BioMCP

    genomoncology
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    maintenance
    Provides LLMs with structured access to critical biomedical databases including PubTator3 (PubMed/PMC), ClinicalTrials.gov, and MyVariant.info through the Model Context Protocol.
    35
    591
    MIT

  • BCI-MCP Server

    enkhbold470
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    license
    A
    quality
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    maintenance
    A framework that integrates Brain-Computer Interface technology with the Model Context Protocol to enable real-time neural signal processing and AI-powered interactions for healthcare, accessibility, and research applications.
    12
    16
    MIT