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  • FLASK-tools by FLASK-LLNL

    FLASK-toolsofficial

    FLASK-LLNL
    F
    license
    Not graded
    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
    Not graded
    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
    Not graded
    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
  • bio-mcp-evo2 by bio-mcp

    bio-mcp-evo2official

    bio-mcp
    A
    license
    Not graded
    quality
    D
    maintenance
    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.
    MIT

  • 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

  • BioBTree

    tamerh
    A
    license
    Not graded
    quality
    A
    maintenance
    A unified biomedical graph database that integrates 50+ primary data sources — genes, proteins, compounds, diseases, pathways, and clinical data — into a single queryable graph with billions of cross-reference edges. Its native MCP server gives LLMs direct access to structured, authoritative biomedical data, complementing their reasoning with reliable identifiers and up-to-date database content.
    19
    AGPL 3.0

  • Redis Graph MCP Server

    yskale
    F
    license
    Not graded
    quality
    D
    maintenance
    Enables LLMs and AI agents to query a biomedical knowledge graph stored in RedisGraph, with tools for concept search, synonym enrichment, and study variable discovery through semantic relationships.

  • ESMfold MCP Server

    MacromNex
    F
    license
    Not graded
    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

  • 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

  • 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

  • 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

  • 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