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  • PDBe MCP Servers by PDBeurope

    PDBe MCP Serversofficial

    PDBeurope
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    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.
    Last updated
    33
    36
    Apache 2.0

  • cxg-census-mcp

    MaxMLang
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    license
    B
    quality
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    Enables LLM agents to query the CZ CELLxGENE Census single-cell atlas with ontology-aware filters, cost caps, and full provenance, allowing natural language questions about cell types, tissues, and gene expression.
    Last updated
    13
    MIT
  • Bio-MCP FastQC Server by bio-mcp

    Bio-MCP FastQC Serverofficial

    bio-mcp
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    Enables AI assistants to perform quality control analysis on high-throughput sequencing data using FastQC and MultiQC. It supports single-file and batch processing of FASTQ/FASTA files and generates comprehensive, interactive summary reports.
    Last updated
    MIT
  • bio-mcp-evo2 by bio-mcp

    bio-mcp-evo2official

    bio-mcp
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    An MCP server that enables AI assistants to generate, score, and analyze DNA sequences using the evo2 genomic foundation model. It supports multiple execution modes including local GPU, SLURM clusters, and the Nvidia NIM cloud API for tasks like variant effect prediction and sequence embedding.
    Last updated
    MIT

  • BWA MCP Server

    bio-mcp
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    Enables AI assistants to perform DNA/RNA sequence alignment using BWA (Burrows-Wheeler Aligner), supporting both short and long read alignment to reference genomes with indexing, BWA-MEM, and BWA-backtrack algorithms.
    Last updated
    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

  • uniprot-mcp

    fzlzjerry
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    quality
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    MCP server that exposes the UniProt REST API to LLM clients, enabling search and retrieval of protein data via tools like search_uniprotkb, get_entry, and map_ids.
    Last updated
    7
    MIT

  • Rosetta MCP Server

    Arielbs
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    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.
    Last updated
    19
    238
    16
    MIT

  • mcp-ubergraph-query

    twhetzel
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    Enables AI assistants to query the Ubergraph biomedical ontology SPARQL endpoint with tools for custom SPARQL queries, term lookup, search, and hierarchy traversal.
    Last updated
    4
    MIT
  • openpgx by open-pgx

    openpgxofficial

    open-pgx
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    quality
    D
    maintenance
    Enables AI-driven pharmacogenomic analysis by querying structured genetic variant, drug response, and disease risk data. Supports natural language questions about medications, traits, and health risks based on user genome data, with privacy-first local execution.
    Last updated
    16
    90
    10
    MIT

  • BioNext-mcp

    Cherine0205
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    A
    quality
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    maintenance
    Enables bioinformatics analysis through natural language conversations with Claude Desktop, automatically generating and executing Python scripts to produce HTML reports and visualizations.
    Last updated
    3
    5
    8
    MIT