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"Connecting to and Running Queries on Local and Remote Databases" matching MCP servers:

  • Biomart MCP

    jzinno
    A
    license
    A
    quality
    D
    maintenance
    A Model Context Protocol server that interfaces with Biomart databases, allowing models to discover biological datasets, explore attributes/filters, retrieve biological data, and translate between different biological identifiers.
    8
    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

  • mcp-ubergraph-query

    twhetzel
    A
    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

  • BioMCP

    genomoncology
    A
    license
    A
    quality
    A
    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

  • gwas-mcp

    muslus
    A
    license
    C
    quality
    F
    maintenance
    Provides AI-powered access to major biological databases for GWAS and bioinformatics research. Enables natural language queries for protein, gene, variant, pathway, and drug discovery analysis.
    44
    1
    MIT

  • PubTator-MCP-Server

    JackKuo666
    A
    license
    -
    quality
    D
    maintenance
    šŸ” A biomedical literature annotation and relationship mining server based on PubTator3, providing convenient access through the MCP interface.
    9
    MIT

  • gget-mcp

    longevity-genie
    A
    license
    -
    quality
    F
    maintenance
    An MCP server for the gget bioinformatics library that enables AI assistants to perform complex genomics queries, including gene sequence retrieval, BLAST alignments, and protein structure predictions.
    30
    MIT

  • pgx-mcp

    Julius-Schmidt
    A
    license
    -
    quality
    D
    maintenance
    Enables real-time pharmacogenomics analysis, including variant clinical significance, drug-gene interactions, and dosing guidelines, by connecting to ClinVar, PharmGKB, gnomAD, and other databases.
    1
    MIT

  • GenomeMCP

    Eldergenix
    A
    license
    -
    quality
    D
    maintenance
    Enables AI agents to query clinical genomics databases, retrieve supporting literature, analyze population genetics, and visualize biological pathways.
    22
    MIT

  • TogoMCP

    arkinjo
    A
    license
    -
    quality
    F
    maintenance
    Executes SPARQL queries against biological and biomedical RDF databases from the RDF Portal, with additional REST API integrations for bioinformatics resources.
    1
    MIT

  • ncbi-mcp

    QiGoki
    A
    license
    -
    quality
    D
    maintenance
    A server providing access to NCBI E-utilities API for searching and retrieving data from databases like PubMed, Protein, and Nucleotide.
    MIT

  • @cyanheads/uniprot-mcp-server

    cyanheads
    A
    license
    -
    quality
    A
    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

  • tacc-mcp-bio

    Narasimhan-Lab
    F
    license
    -
    quality
    C
    maintenance
    Enables Claude Code to interact with a TACC or SLURM HPC cluster for bioinformatics pipelines, allowing job management, log reading, file browsing, remote script execution, and job submission through natural language.