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"Methods for Conducting In-Depth Online Searches" matching MCP servers:

  • methods-mcp

    webwebb56
    A
    license
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    quality
    D
    maintenance
    Provides MCP tool adapters for Bioconductor methods like limma, DESeq2, and fgsea, enabling statistical analysis of omics data through containerized R execution. It serves as a bridge between MCP clients and bioinformatics tools for reproducible research workflows.
    Apache 2.0
  • 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
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    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

  • BioMCP

    acashmoney
    F
    license
    B
    quality
    D
    maintenance
    A Model Context Protocol server that enhances language models with protein structure analysis capabilities, enabling detailed active site analysis and disease-related protein searches through established protein databases.
    2
    18
  • Bio-MCP BLAST by bio-mcp

    Bio-MCP BLASTofficial

    bio-mcp
    A
    license
    -
    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

  • 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

  • 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

  • hpo-link

    berntpopp
    A
    license
    A
    quality
    A
    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.
    17
    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