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  • uniprot-link

    berntpopp
    A
    license
    A
    quality
    A
    maintenance
    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.
    15
    MIT
  • Cytoscape MCP Server by cytoscape

    Cytoscape MCP Serverofficial

    cytoscape
    A
    license
    Not graded
    quality
    A
    maintenance
    An embedded MCP server for Cytoscape Desktop that lets AI agents load networks, set active views, and control the desktop application over HTTP.
    6
    BSD 3-Clause

  • SciAgentKit

    ehsansyh
    A
    license
    Not graded
    quality
    C
    maintenance
    MCP-native scientific skills for reproducible computational biology and AI-driven drug-discovery workflows. It combines deterministic scientific tools with an MCP server to give AI agents real computational capabilities.
    Apache 2.0

  • gget-mcp

    longevity-genie
    A
    license
    Not graded
    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

  • UniProt MCP Server

    vitamin3615
    A
    license
    Not graded
    quality
    D
    maintenance
    An MCP server that enables language models to fetch protein information from the UniProt database, including protein details, sequences, functions, and structures.
    MIT

  • VepClin-MCP

    shivankvirdi
    F
    license
    Not graded
    quality
    B
    maintenance
    A terminal-based bioinformatics CLI chat tool that integrates Ensembl VEP, NCBI ClinVar, an MCP server layer, and OpenRouter's NVIDIA Nemotron 3 Ultra model to provide variant consequence and clinical significance lookups with clear summaries in a Rich-powered CLI.

  • pymol-cursor-mcp

    truong128
    F
    license
    Not graded
    quality
    D
    maintenance
    Control PyMOL from Cursor via natural language. Enables describing molecular structures and styles in plain language to execute PyMOL commands through XML-RPC.
    1

  • OrigeneMCP

    GENTEL-lab
    F
    license
    Not graded
    quality
    D
    maintenance
    An advanced integrated MCP server platform that combines 600+ tools and multiple biomedical databases to enable comprehensive information retrieval across molecules, proteins, genes, and diseases for accelerating therapeutic research.
    38

  • hgnc-link

    berntpopp
    A
    license
    A
    quality
    A
    maintenance
    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.
    9
    MIT

  • ChemCP

    scottmreed
    A
    license
    A
    quality
    D
    maintenance
    Renders interactive 2D molecular structure diagrams from SMILES notation and computes molecular properties like molecular weight, LogP, and TPSA, directly in the chat.
    1
    60
    1
    ISC

  • 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

  • nucleotide_archive_mcp

    biocontext-ai
    A
    license
    A
    quality
    C
    maintenance
    An MCP server for searching and accessing RNA sequencing datasets from the European Nucleotide Archive (ENA), supporting bulk, single-cell, and spatial transcriptomics with advanced filtering and download capabilities.
    11
    1
    Apache 2.0

  • mgi-link

    berntpopp
    A
    license
    A
    quality
    A
    maintenance
    An MCP server that provides mouse genetics data from Mouse Genome Informatics (MGI), enabling LLM agents to query markers, mutations, alleles, phenotypes, and disease models.
    13
    1
    MIT