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"Methods and Tools for Extracting Paper Summaries" matching MCP servers:

  • methods-mcp

    webwebb56
    A
    license
    -
    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

  • paper-search-mcp

    upascal
    F
    license
    -
    quality
    C
    maintenance
    Enables searching for academic papers and preprints across multiple platforms including Semantic Scholar, arXiv, PubMed, and CrossRef. It provides access to research records, DOI lookups, and journal metadata through a unified interface deployed on Cloudflare Workers.
  • 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
    -
    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
    -
    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

  • pubchem-mcp-server

    cyanheads
    A
    license
    A
    quality
    A
    maintenance
    Enables AI agents and applications to search, retrieve, and analyze chemical compounds, substances, and bioassays from PubChem's vast chemical information database through comprehensive tools for chemical research and discovery.
    10
    404
    9
    Apache 2.0

  • mcp-alphafold

    zeinab-sheikhi
    F
    license
    B
    quality
    D
    maintenance
    Provides programmatic access to AlphaFold protein structure predictions and UniProt data, enabling users to retrieve protein structures, summaries, and annotations through natural language.
    3

  • MolMIM MCP Server

    siarhei-fedziukovich
    A
    license
    -
    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

  • PomBase MCP Server

    ubcd-ibfg
    A
    license
    -
    quality
    C
    maintenance
    Enables AI agents to query the fission yeast PomBase database for gene summaries, GO annotations, phenotypes, orthologs, domains, and interactions via structured API calls.
    MIT

  • mcp-alphafold

    pipeworx-io
    A
    license
    -
    quality
    C
    maintenance
    Provides access to AlphaFold predicted protein 3D structures from EBI, enabling retrieval of prediction metadata, summaries, annotations, and UniProt data.
    19
    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

  • 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