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Bioinformatics

Tools for computational analysis of biological data, including genomics, proteomics, and other molecular biology data. Enables access to bioinformatics pipelines, algorithms, and databases.

MCP ServersBrowse all →

  • Noctua MCP Server by geneontology

    Noctua MCP Serverofficial

    geneontology
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    Enables editing and querying of Gene Ontology Causal Activity Models (GO-CAMs) through the Barista API. Supports model creation, individual and fact management, evidence addition, and causal pathway construction for biological knowledge representation.
    Last updated
    18
    BSD 3-Clause

  • STRING-MCP

    MCPmed
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    license
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    quality
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    A Model Context Protocol server that provides tools for interacting with the STRING database to analyze protein-protein interaction networks and functional enrichment. It enables users to map protein identifiers, retrieve interaction data, and generate biological network visualizations through natural language interfaces.
    Last updated
    11
    3
    BSD 3-Clause

  • Rowan MCP Server

    k-yenko
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    license
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    quality
    D
    maintenance
    Enables molecular design and simulation through 45 chemistry tools including pKa calculations, geometry optimization, conformer searches, docking, protein cofolding, and ADMET predictions powered by Rowan's computational chemistry platform.
    Last updated
    41
    23
    MIT

  • 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

  • gnomAD MCP Server

    koido
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    license
    B
    quality
    B
    maintenance
    Provides a programmatic interface to the Genome Aggregation Database (gnomAD) API across versions v2.1.1, v3.1.2, and v4.1.0. It enables users to query gene metadata, variant information, population frequencies, and ClinVar data through a unified schema.
    Last updated
    12
    5
    Apache 2.0

  • MCP Sequence Simulation Server

    coreymhudson
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    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.
    Last updated
    6
    BSD 2-Clause "Simplified"

  • Protein MCP Server

    gqy20
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    Enables searching, retrieving, and downloading protein structure data from the RCSB Protein Data Bank. Supports intelligent protein structure search, comprehensive data retrieval, and multiple file format downloads for bioinformatics research.
    Last updated
    3
    MIT

  • Biomart MCP

    jzinno
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    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.
    Last updated
    8
    7
    MIT

  • MCP PubMed Search

    wavelovey
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    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.
    Last updated
    1
    47
    MIT

  • AlphaGenome MCP Server

    taehojo
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    quality
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    Enables AI-powered genomic variant analysis including variant impact prediction, regulatory element discovery, and batch variant scoring. Currently operates in mock mode as a proof-of-concept awaiting the public release of Google DeepMind's AlphaGenome API.
    Last updated
    20
    9
    2
    MIT

  • Enrichr MCP Server

    tianqitang1
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    license
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    quality
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    Enables gene set enrichment analysis using the Enrichr API across hundreds of gene set libraries including Gene Ontology, pathways, diseases, tissues, drugs, and transcription factors. Returns only statistically significant results for interpretation.
    Last updated
    2
    213
    14
    MIT

  • BioPython MCP Server

    kmaneesh
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    license
    B
    quality
    B
    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.
    Last updated
    32
    2
    MIT

  • STRING MCP Server

    munch-group
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    license
    B
    quality
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    Provides access to the STRING protein-protein interaction database for mapping identifiers, retrieving interaction networks, and performing functional enrichment analysis. It enables users to explore protein partners, pathways, and cross-species homology through natural language interactions.
    Last updated
    9
    ISC

  • BioMCP

    genomoncology
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    maintenance
    Provides LLMs with structured access to critical biomedical databases including PubTator3 (PubMed/PMC), ClinicalTrials.gov, and MyVariant.info through the Model Context Protocol.
    Last updated
    35
    497

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