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  • Omics AI MCP Server

    mfiume
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    Enables AI agents to conversationally interact with genomics research networks for data analysis and discovery across multiple Omics AI Explorer platforms. It provides tools for exploring data collections, examining table schemas, and executing SQL queries against datasets like Viral AI and Neuroscience AI.
    Last updated
    6
    1
    MIT

  • uniprot-link

    berntpopp
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    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.
    Last updated
    15
    MIT

  • hgnc-link

    berntpopp
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    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.
    Last updated
    9
    MIT

  • metadome-link

    berntpopp
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    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.
    Last updated
    11
    MIT

  • rnaseq-mcp

    sbarbi-gh
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    quality
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    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.
    Last updated
    7

  • WetLab-MCP

    muslus
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    Enables AI-assisted molecular biology experiment design with tools for qPCR primer design, cloning strategy optimization, TaqMan probe design, and multiplex compatibility analysis.
    Last updated
    6
    1
    MIT

  • hpo-link

    berntpopp
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    quality
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    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.
    Last updated
    17
    MIT

  • Rosetta MCP Server

    Arielbs
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    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.
    Last updated
    19
    238
    16
    MIT
  • PDBe MCP Servers by PDBeurope

    PDBe MCP Serversofficial

    PDBeurope
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    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.
    Last updated
    33
    36
    Apache 2.0

  • mcp-ubergraph-query

    twhetzel
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    Enables AI assistants to query the Ubergraph biomedical ontology SPARQL endpoint with tools for custom SPARQL queries, term lookup, search, and hierarchy traversal.
    Last updated
    4
    MIT

  • TogoMCP

    dbcls
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    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).
    Last updated
    29
    9
    MIT

  • plant-genomics-mcp

    musharna
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    ▎ 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.
    Last updated
    32
    3
    MIT
  • openpgx by open-pgx

    openpgxofficial

    open-pgx
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    quality
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    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.
    Last updated
    16
    90
    10
    MIT