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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 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
  • Bio-MCP BLAST by bio-mcp

    Bio-MCP BLASTofficial

    bio-mcp
    A
    license
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    quality
    D
    maintenance
    Enables AI assistants to perform NCBI BLAST sequence similarity searches through natural language, supporting nucleotide and protein searches, custom database creation, and multiple output formats.
    10
    MIT

  • mcp-gwas-catalog

    pipeworx-io
    A
    license
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    quality
    C
    maintenance
    MCP server for querying the GWAS Catalog (EBI/NHGRI), a curated catalog of genome-wide association studies. It enables AI agents to search and retrieve study data via natural language or direct tool calls.
    4
    MIT

  • Scanpy-MCP

    scmcphub
    A
    license
    -
    quality
    C
    maintenance
    Provides a natural language interface for scRNA-Seq analysis using the Scanpy library, supporting operations such as data preprocessing, clustering, and visualization. It enables AI agents and clients to perform complex single-cell transcriptomics workflows through the Model Context Protocol.
    2
    BSD 3-Clause

  • string-mcp

    meringlab
    A
    license
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    quality
    A
    maintenance
    MCP server that exposes STRING database functionality, allowing AI agents to resolve protein identifiers, retrieve interaction networks, perform homology lookups, and run functional enrichment analysis.
    5
    MIT

  • gget-mcp

    longevity-genie
    A
    license
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    quality
    F
    maintenance
    An MCP server for the gget bioinformatics library that enables AI assistants to perform complex genomics queries, including gene sequence retrieval, BLAST alignments, and protein structure predictions.
    30
    MIT

  • mcp-uniprot

    pipeworx-io
    A
    license
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    quality
    C
    maintenance
    Provides access to UniProt protein sequence and function knowledge base, enabling search and retrieval of protein entries, proteomes, taxonomy, and feature annotations.
    7
    MIT

  • MOF Tools MCP Server

    liuyuxiang92
    A
    license
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    quality
    D
    maintenance
    A specialized MCP server for Metal-Organic Framework research that provides tools for database searching, structural optimization, and energy calculations via ASE. It enables scientific workflows by allowing users to interact with MOF data and perform chemical simulations through a standard SSE interface.
    MIT

  • heracleum-tox-mcp-server

    chemagents
    A
    license
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    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

  • decoupler-MCP

    scmcphub
    F
    license
    -
    quality
    C
    maintenance
    Provides a natural language interface for single-cell RNA-Seq analysis using the decoupleR framework. It enables users to perform biological pathway inference, data clustering, and visualization through MCP-compatible AI clients.
    4

  • BioOpenMCP

    JesKwek
    F
    license
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    quality
    D
    maintenance
    BioOpenMCP enables users to run bioinformatics tools like FastQC, Cutadapt, and STAR with background execution and status checking. It integrates with Claude Desktop to perform quality control, trimming, alignment, and reporting via natural language.
    1

  • bioRxiv-MCP-Server

    JackKuo666
    F
    license
    -
    quality
    F
    maintenance
    🔍 Enable AI assistants to search and access bioRxiv papers through a simple MCP interface. The bioRxiv MCP Server provides a bridge between AI assistants and bioRxiv's preprint repository through the Model Context Protocol (MCP). It allows AI models to search for biology preprints and access their
    24

  • Infercnv-MCP

    scmcphub
    F
    license
    -
    quality
    C
    maintenance
    Provides a natural language interface for inferring Copy Number Variations (CNVs) from scRNA-Seq data using the infercnvpy framework. It enables users to perform data preprocessing, CNV inference, and visualization through chromosome heatmaps, UMAP, and t-SNE plots.
    2

  • paper-search-mcp

    upascal
    F
    license
    -
    quality
    C
    maintenance
    Enables searching for academic papers and preprints across multiple platforms including Semantic Scholar, arXiv, PubMed, and CrossRef. It provides access to research records, DOI lookups, and journal metadata through a unified interface deployed on Cloudflare Workers.