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  • BioMCP

    yeyuan98
    A
    license
    A
    quality
    D
    maintenance
    A high-performance MCP server that gives LLMs access to 25 biomedical tools federated across 50+ upstream APIs for genes, variants, drugs, diseases, literature, clinical trials, and structural biology.
    25
    67
    2
    MIT
  • galaxy-mcp by galaxyproject

    galaxy-mcpofficial

    galaxyproject
    A
    license
    Not graded
    quality
    A
    maintenance
    MCP server for interacting with Galaxy bioinformatics platform, enabling AI assistants to connect to Galaxy instances, search and execute tools, manage workflows, and access other features.
    37
    MIT

  • mcp-gwas-catalog

    pipeworx-io
    A
    license
    Not graded
    quality
    C
    maintenance
    MCP server for querying the GWAS Catalog (EBI/NHGRI), a curated catalog of genome-wide association studies. It enables AI agents to search and retrieve study data via natural language or direct tool calls.
    4
    MIT

  • mcp-pombase

    pipeworx-io
    A
    license
    Not graded
    quality
    C
    maintenance
    Enables AI agents to query the PomBase fission yeast model-organism database for genetic and molecular data through the Pipeworx MCP gateway.
    4
    MIT

  • mcp-mygene-info

    pipeworx-io
    A
    license
    Not graded
    quality
    C
    maintenance
    MCP server for querying gene annotations, full-text gene search, and species taxonomy via MyGene.info. Enables AI agents to access gene data through natural language questions.
    14
    MIT

  • mcp-interpro

    pipeworx-io
    A
    license
    Not graded
    quality
    C
    maintenance
    This server provides access to InterPro protein family, domain, and functional-site classification data from EBI. It allows querying protein annotations through natural language or direct tool calls.
    4
    MIT

  • mcp-uniprot

    pipeworx-io
    A
    license
    Not graded
    quality
    C
    maintenance
    Provides access to UniProt protein sequence and function knowledge base, enabling search and retrieval of protein entries, proteomes, taxonomy, and feature annotations.
    7
    MIT

  • mcp-bioregistry

    pipeworx-io
    A
    license
    Not graded
    quality
    C
    maintenance
    Provides tools to query and resolve identifiers from the Bioregistry, including prefix metadata, CURIE resolution, and substring search.
    9
    MIT

  • mcp-alphafold

    pipeworx-io
    A
    license
    Not graded
    quality
    C
    maintenance
    Provides access to AlphaFold predicted protein 3D structures from EBI, enabling retrieval of prediction metadata, summaries, annotations, and UniProt data.
    19
    MIT

  • expression-atlas

    pipeworx-io
    A
    license
    Not graded
    quality
    C
    maintenance
    Enables querying the EBI Expression Atlas for gene expression data across species and conditions. Part of the Pipeworx gateway, it provides access to baseline and differential expression studies.
    7
    MIT

  • heracleum-tox-mcp-server

    chemagents
    A
    license
    Not graded
    quality
    B
    maintenance
    Reproduces the in-silico toxicological profile of Heracleum sosnowskyi metabolites from Rassabina & Fedorov (2025) using open-source models for LD50 prediction, toxicity classification, chemical space clustering, and synthesis cost estimation.
    MIT

  • 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

  • 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
    602
    MIT

  • BioNext-mcp

    Cherine0205
    A
    license
    A
    quality
    D
    maintenance
    Enables bioinformatics analysis through natural language conversations with Claude Desktop, automatically generating and executing Python scripts to produce HTML reports and visualizations.
    3
    13
    9
    MIT

  • PDB MCP Server

    Augmented-Nature
    F
    license
    A
    quality
    F
    maintenance
    A Model Context Protocol (MCP) server that provides access to the Protein Data Bank (PDB) - the worldwide repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.
    5
    25