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"Tools and Templates for Prompt Management and Workflow Automation" matching MCP servers:

  • 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
  • CEDAR MCP Server by musen-lab

    CEDAR MCP Serverofficial

    musen-lab
    A
    license
    A
    quality
    A
    maintenance
    Enables interaction with the CEDAR metadata repository, including fetching templates, searching BioPortal ontology terms, and managing template instances.
    8
    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

  • Bio-OS MCP Server

    GBA-BI
    A
    license
    C
    quality
    B
    maintenance
    Enables workflow management and Docker image building for Bio-OS platform. Supports WDL workflow submission, validation, and monitoring, along with Docker image building and status tracking for bioinformatics workflows.
    22
    5
    MIT

  • kegg-mcp

    AriaShishegaran
    A
    license
    Not graded
    quality
    B
    maintenance
    An MCP server that exposes the KEGG REST API — pathways, genes, compounds, reactions, enzymes, diseases, drugs, modules, orthology, glycans, and BRITE hierarchies, with cross-database linking. Provides 34 tools and 8 resource templates.
    MIT

  • refua-mcp

    agentcures
    A
    license
    Not graded
    quality
    C
    maintenance
    MCP server for biological protein design, folding, and affinity prediction using Refua tools, with optional support for ADMET, clinical simulation, preclinical planning, wet-lab automation, and more.
    MIT

  • gene-family-mcp

    xxay-16
    F
    license
    Not graded
    quality
    B
    maintenance
    MCP server for gene family analysis, providing tools for FASTA validation and PlantCARE cis-element prediction, with backend task management for AI agents.

  • Chai-1 MCP Server

    MacromNex
    F
    license
    Not graded
    quality
    D
    maintenance
    Enables protein structure prediction using the Chai-1 model via Docker, with tools for small peptides, FASTA-based predictions, MSA-enhanced predictions, batch processing, and job management.

  • 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

  • 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
  • Noctua MCP Server by geneontology

    Noctua MCP Serverofficial

    geneontology
    A
    license
    A
    quality
    C
    maintenance
    Enables editing and querying of Gene Ontology Causal Activity Models (GO-CAMs) through the Barista API. Supports model creation, individual and fact management, evidence addition, and causal pathway construction for biological knowledge representation.
    18
    BSD 3-Clause