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"An Integrated Development Environment (IDE) for programming" matching MCP servers:

  • OrigeneMCP

    GENTEL-lab
    F
    license
    -
    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

  • ESMfold MCP Server

    MacromNex
    F
    license
    -
    quality
    D
    maintenance
    Enables protein sequence analysis and structure prediction by extracting ESM-2 embeddings and batch processing FASTA files via Docker. It provides tools for large-scale embedding extraction, job monitoring, and model management within an MCP-compatible environment.

  • 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

  • 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

  • Gigwa-MCP

    gkanogiannis
    A
    license
    A
    quality
    A
    maintenance
    An MCP server that interfaces with Gigwa for genotyping data import, analysis, and audit, enabling users to perform complex workflows through natural language commands.
    29
    Apache 2.0

  • Rosetta MCP Server

    Arielbs
    A
    license
    A
    quality
    F
    maintenance
    An MCP server that enables AI coding assistants to interact with Rosetta, PyRosetta, and Biotite for running RosettaScripts, validating XML, translating between Rosetta and Biotite, scoring structures, and querying documentation.
    19
    112
    18
    MIT

  • TogoMCP

    dbcls
    A
    license
    A
    quality
    A
    maintenance
    An MCP server that gives AI assistants access to biological and biomedical RDF databases via SPARQL at the RDF Portal, as well as selected REST APIs (NCBI E-utilities, UniProt, ChEMBL, PDB, Reactome, Rhea, MeSH, and more).
    29
    11
    MIT

  • ncbi-datasets-mcp

    syntheticgio
    F
    license
    A
    quality
    A
    maintenance
    An MCP server that gives Claude access to NCBI Datasets v2 — search genome assembly metadata, retrieve taxonomy records, and download data packages without leaving your conversation.
    10

  • 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

  • metabo-idmapper

    Wooyoung-kim91
    A
    license
    A
    quality
    B
    maintenance
    Converts messy metabolite names into standard database identifiers (KEGG, HMDB, ChEBI, PubChem, InChIKey) and performs crosswalking to Mouse-GEM for metabolic model input, with deterministic tools and an LLM reasoning layer for identity disambiguation.
    20
    MIT

  • 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

  • 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