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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

  • genefoundry

    berntpopp
    A
    license
    Not graded
    quality
    A
    maintenance
    Federates 13 gene-related MCP backends (gnomAD, GTEx, etc.) behind a single Streamable HTTP endpoint with collision-free namespacing and search-based tool discovery.
    2
    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

  • kegg-mcp-server

    Lucas-Servi
    A
    license
    A
    quality
    A
    maintenance
    An MCP server for querying the KEGG bioinformatics database, providing tools, resource templates, and guided prompts for pathways, genes, compounds, and more.
    34
    3
    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

  • 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

  • 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

  • Omics AI MCP Server

    mfiume
    A
    license
    A
    quality
    D
    maintenance
    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.
    6
    1
    MIT

  • MCP Sequence Simulation Server

    coreymhudson
    A
    license
    A
    quality
    D
    maintenance
    Enables the generation, mutation, and evolution of DNA and protein sequences using various evolutionary models and phylogenetic algorithms. It supports realistic next-generation sequencing read simulation and population-level evolutionary tracking for bioinformatics research and testing.
    6
    BSD 2-Clause "Simplified"

  • 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

  • BioPython MCP Server

    kmaneesh
    A
    license
    B
    quality
    C
    maintenance
    Provides comprehensive BioPython capabilities for biological sequence analysis, alignment, database access (GenBank, UniProt, PubMed), protein structure analysis, and phylogenetics through a Model Context Protocol interface for AI-assisted bioinformatics workflows.
    32
    3
    MIT

  • STRING-db MCP Server

    Augmented-Nature
    F
    license
    B
    quality
    D
    maintenance
    A comprehensive Model Context Protocol (MCP) server for accessing the STRING protein interaction database. This server provides powerful tools for protein network analysis, functional enrichment, and comparative genomics through the STRING API.
    6
    4

  • 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

  • gnomAD MCP Server

    shukwong
    F
    license
    B
    quality
    D
    maintenance
    Enables AI assistants to query genetic variant data, gene constraints, and population genetics information from the gnomAD (Genome Aggregation Database) through its GraphQL API. Supports searching for genes and variants, retrieving constraint scores, analyzing population frequencies, and accessing genomic coverage data.
    9
    10

  • 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

  • Bio-OS MCP Server

    GBA-BI
    A
    license
    C
    quality
    B
    maintenance
    Enables workflow management and Docker image building for Bio-OS platform. Supports WDL workflow submission, validation, and monitoring, along with Docker image building and status tracking for bioinformatics workflows.
    22
    5
    MIT