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  • PDBe MCP Servers by PDBeurope

    PDBe MCP Serversofficial

    PDBeurope
    A
    license
    B
    quality
    A
    maintenance
    Provides seamless access to the Protein Data Bank in Europe (PDBe) API and search capabilities, enabling AI clients to query protein structures, perform advanced searches, and retrieve structural biology data.
    33
    37
    Apache 2.0

  • MCP LAMMPS Server

    Chenghao-Wu
    A
    license
    -
    quality
    F
    maintenance
    A Model Context Protocol server that enables AI assistants to interact with LAMMPS for molecular dynamics simulations through natural language commands.
    14
    Apache 2.0
  • FLASK-tools by FLASK-LLNL

    FLASK-toolsofficial

    FLASK-LLNL
    F
    license
    -
    quality
    B
    maintenance
    Provides a collection of MCP servers for computational chemistry tasks including molecular generation and retrosynthesis. Also offers property prediction and molecule pricing capabilities.

  • Redis Graph MCP Server

    yskale
    F
    license
    -
    quality
    D
    maintenance
    Enables LLMs and AI agents to query a biomedical knowledge graph stored in RedisGraph, with tools for concept search, synonym enrichment, and study variable discovery through semantic relationships.

  • 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

  • rnaseq-mcp

    sbarbi-gh
    F
    license
    A
    quality
    C
    maintenance
    Enables analysis of bulk RNA-seq data using natural language queries, executing R and Python in a Docker container with automatic sample anonymization and privacy controls.
    7

  • 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

  • plant-genomics-mcp

    musharna
    A
    license
    A
    quality
    A
    maintenance
    ▎ Provides 32 tools for plant-genomics locus lookup across 11 free public backends (Ensembl Plants, Phytozome, UniProtKB, Europe PMC, QuickGO, NCBI BLAST, Gramene, KEGG, STRING-DB, ATTED-II, BAR). Takes a TAIR-style locus plus optional organism and returns gene metadata, functional/pathway annotation, interactions, co-expression, and literature — in single-locus, batch, and cross-source synthesis.
    50
    3
    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

  • 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