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  • Bio_MCP

    ricancong
    F
    license
    B
    quality
    C
    maintenance
    Enables users to generate volcano plots by submitting jobs with input files and parameters, supporting local or Docker execution.
    8
    1

  • 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

  • hpo-link

    berntpopp
    A
    license
    A
    quality
    A
    maintenance
    MCP server that provides tools for querying the Human Phenotype Ontology (HPO) including term lookup, hierarchy exploration, cross-ontology mappings, and gene-phenotype-disease associations, all grounded in a local SQLite database for fast offline lookups.
    17
    MIT

  • AlphaFold Sovereign MCP

    smaniches
    A
    license
    A
    quality
    A
    maintenance
    Integrates AlphaFold DB and eight other biomedical data sources into MCP tools for variant clinical reporting, disease-target analysis, structural intelligence, and drug repurposing, with results persisted to a local SQLite knowledge graph.
    30
    4
    Apache 2.0

  • 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
  • openpgx by open-pgx

    openpgxofficial

    open-pgx
    A
    license
    A
    quality
    D
    maintenance
    Enables AI-driven pharmacogenomic analysis by querying structured genetic variant, drug response, and disease risk data. Supports natural language questions about medications, traits, and health risks based on user genome data, with privacy-first local execution.
    16
    455
    11
    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

  • 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

  • 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

  • Wegene Assistant MCP Server

    xraywu
    F
    license
    A
    quality
    D
    maintenance
    Leverages large language models to analyze users' WeGene genetic testing reports, providing access to report data via custom URI schemes and enabling profile and report management through OAuth authentication and API utilization.
    4
    4

  • UniProt MCP Server

    josefdc
    A
    license
    B
    quality
    D
    maintenance
    Provides seamless access to UniProtKB protein database, enabling queries for protein entries, sequences, Gene Ontology annotations, full-text search, and ID mapping across 200+ database types.
    5
    2
    MIT

  • paperSearch

    FreddieWho
    A
    license
    B
    quality
    A
    maintenance
    Enables AI coding agents to search academic papers, resolve biomedical entities, mine relations, and traverse citation graphs using Semantic Scholar and PubTator3, with local caching for reproducibility.
    11
    MIT

  • 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