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"Local RAG system for providing documentation to a large language model (LLM)" matching MCP servers:

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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.
    8
    8
    MIT
  • A
    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.
    19
    112
    18
    MIT
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    A
    quality
    B
    maintenance
    Converts messy metabolite names into standard database identifiers (KEGG, HMDB, ChEBI, PubChem, InChIKey) and performs crosswalking to Mouse-GEM for metabolic model input, with deterministic tools and an LLM reasoning layer for identity disambiguation.
    20
    MIT
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    A Model Context Protocol server providing LLMs with access to the Ensembl genomics database, enabling AI assistants to query gene information, sequences, variants, and other genomic data across multiple species.
    10
    8
    JavaScript
    MIT
  • F
    license
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    Leverages large language models to analyze users' WeGene genetic testing reports, providing access to report data via custom URI schemes and enabling profile and report management through OAuth authentication and API utilization.
    4
    4
  • A
    license
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    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.
    13
    MIT
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    quality
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    A Model Context Protocol server that provides tools for interacting with the STRING database to analyze protein-protein interaction networks and functional enrichment. It enables users to map protein identifiers, retrieve interaction data, and generate biological network visualizations through natural language interfaces.
    11
    3
    BSD 3-Clause
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    quality
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    Enables running GROMACS molecular dynamics simulations through natural language, with tools for topology building, solvation, simulation management, and trajectory processing via the Model Context Protocol.
    31
    MIT
  • F
    license
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    A Model Context Protocol server that enhances language models with protein structure analysis capabilities, enabling detailed active site analysis and disease-related protein searches through established protein databases.
    2
    18
  • A
    license
    C
    quality
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    maintenance
    A Model Context Protocol server that lets you drive PyMOL with natural language, enabling structure loading, analytical views, measurements, and protein exploration through AI assistants.
    100
    15
    MIT
  • A
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    Not graded
    quality
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    maintenance
    Enables AI agents to control RELION 5.x cryo-EM structure determination software through natural language, providing 23 tools for the complete single-particle analysis pipeline.
    4
    MIT
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    maintenance
    MCP server for querying the GWAS Catalog (EBI/NHGRI), a curated catalog of genome-wide association studies. It enables AI agents to search and retrieve study data via natural language or direct tool calls.
    4
    MIT
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    Not graded
    quality
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    maintenance
    Provides a natural language interface for scRNA-Seq analysis using the Scanpy library, supporting operations such as data preprocessing, clustering, and visualization. It enables AI agents and clients to perform complex single-cell transcriptomics workflows through the Model Context Protocol.
    2
    BSD 3-Clause