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  • nucleotide_archive_mcp

    biocontext-ai
    A
    license
    A
    quality
    C
    maintenance
    An MCP server for searching and accessing RNA sequencing datasets from the European Nucleotide Archive (ENA), supporting bulk, single-cell, and spatial transcriptomics with advanced filtering and download capabilities.
    11
    1
    Apache 2.0

  • biothings-mcp

    longevity-genie
    A
    license
    A
    quality
    F
    maintenance
    Provides a Model Context Protocol server for accessing and querying biomedical data from BioThings services, including gene, variant, chemical, and taxon annotations.
    19
    33
    MIT

  • STRING-db MCP Server

    Augmented-Nature
    F
    license
    B
    quality
    D
    maintenance
    A comprehensive Model Context Protocol (MCP) server for accessing the STRING protein interaction database. This server provides powerful tools for protein network analysis, functional enrichment, and comparative genomics through the STRING API.
    6
    4

  • MCP PubMed Search

    wavelovey
    A
    license
    B
    quality
    D
    maintenance
    Server to search PubMed (PubMed is a free, online database that allows users to search for biomedical and life sciences literature). I have created on a day MCP came out but was on vacation, I saw someone post similar server in your DB, but figured to post mine.
    1
    47
    MIT

  • gnomAD MCP Server

    shukwong
    F
    license
    B
    quality
    D
    maintenance
    Enables AI assistants to query genetic variant data, gene constraints, and population genetics information from the gnomAD (Genome Aggregation Database) through its GraphQL API. Supports searching for genes and variants, retrieving constraint scores, analyzing population frequencies, and accessing genomic coverage data.
    9
    10

  • uniprot-link

    berntpopp
    A
    license
    A
    quality
    A
    maintenance
    An MCP server that grounds protein research in the UniProt SPARQL endpoint, providing tools for querying proteins, sequences, variants, diseases, and more via intent-named tools and raw SPARQL.
    15
    MIT

  • hgnc-link

    berntpopp
    A
    license
    A
    quality
    A
    maintenance
    Grounds gene-nomenclature work in the HUGO Gene Nomenclature Committee (HGNC) dataset, enabling resolution of gene symbols and IDs to canonical HGNC identifiers, plus cross-references and batch operations.
    9
    MIT

  • reactome-mcp

    tc2fh
    A
    license
    A
    quality
    C
    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

  • reactome-db-mcp

    tc2fh
    A
    license
    A
    quality
    C
    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

  • metadome-link

    berntpopp
    A
    license
    A
    quality
    A
    maintenance
    Enables querying of per-residue missense tolerance, Pfam domain annotations, and variant counts for human transcripts by wrapping the MetaDome web service. Provides MCP tools for resolving transcripts, requesting tolerance landscapes, and identifying constrained regions.
    11
    MIT

  • ChemCP

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

  • Rosetta MCP Server

    Arielbs
    A
    license
    A
    quality
    F
    maintenance
    An MCP server that enables AI coding assistants to interact with Rosetta, PyRosetta, and Biotite for running RosettaScripts, validating XML, translating between Rosetta and Biotite, scoring structures, and querying documentation.
    19
    112
    18
    MIT

  • TogoMCP

    dbcls
    A
    license
    A
    quality
    A
    maintenance
    An MCP server that gives AI assistants access to biological and biomedical RDF databases via SPARQL at the RDF Portal, as well as selected REST APIs (NCBI E-utilities, UniProt, ChEMBL, PDB, Reactome, Rhea, MeSH, and more).
    29
    11
    MIT

  • MCP GeneLab Server

    sbl-sdsc
    A
    license
    A
    quality
    B
    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