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  • 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
  • FLASK-tools by FLASK-LLNL

    FLASK-toolsofficial

    FLASK-LLNL
    F
    license
    -
    quality
    B
    maintenance
    Provides a collection of MCP servers for computational chemistry tasks including molecular generation and retrosynthesis. Also offers property prediction and molecule pricing capabilities.

  • scvi-tools MCP Server

    hyennnnnnn
    A
    license
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    quality
    D
    maintenance
    Enables deep probabilistic analysis of single-cell omics data using scvi-tools through natural language. Supports SCVI for scRNA-seq analysis, SCANVI for cell type annotation, TOTALVI for multi-modal RNA/protein data, and PEAKVI for scATAC-seq analysis.
    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

  • BioNext-mcp

    Cherine0205
    A
    license
    A
    quality
    D
    maintenance
    Enables bioinformatics analysis through natural language conversations with Claude Desktop, automatically generating and executing Python scripts to produce HTML reports and visualizations.
    3
    13
    9
    MIT

  • MolMIM MCP Server

    siarhei-fedziukovich
    A
    license
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    quality
    D
    maintenance
    Enables molecular generation, optimization, and analysis through NVIDIA MolMIM API. Supports generating drug-like molecules with desired properties, extracting molecular embeddings, and exploring chemical space around seed molecules.
    MIT

  • BioQC-MCP

    Babajan-B
    A
    license
    -
    quality
    C
    maintenance
    A professional MCP server for comprehensive bioinformatics quality control, providing automated FastQC/MultiQC analysis, HTML report parsing, and advanced data visualization for sequencing data.
    1
    MIT

  • 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

  • metadome-link

    berntpopp
    A
    license
    A
    quality
    A
    maintenance
    Enables querying of per-residue missense tolerance, Pfam domain annotations, and variant counts for human transcripts by wrapping the MetaDome web service. Provides MCP tools for resolving transcripts, requesting tolerance landscapes, and identifying constrained regions.
    11
    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

  • 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

  • WetLab-MCP

    muslus
    A
    license
    A
    quality
    D
    maintenance
    Enables AI-assisted molecular biology experiment design with tools for qPCR primer design, cloning strategy optimization, TaqMan probe design, and multiplex compatibility analysis.
    6
    1
    MIT