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  • A
    license
    Not graded
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    maintenance
    An MCP server providing public plant bioinformatics APIs including UniProt, NCBI, InterProScan, PDB, AlphaFold, Ensembl Plants, and web-based resources like Sol Genomics and BAR, without local data. It supports gene lookups, protein summaries, structure retrieval, and functional annotations through natural language.
    MIT
  • F
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    quality
    A
    maintenance
    Provides a collection of MCP servers for computational chemistry tasks including molecular generation and retrosynthesis. Also offers property prediction and molecule pricing capabilities.
    -
  • A
    license
    B
    quality
    C
    maintenance
    Enables MCP-capable AI clients to characterize proteins end to end: PDB/mmCIF validation, sequence extraction and typing, pLDDT confidence summaries, metal-site geometry with bidentate chelate detection, GROMACS trajectory metrics and plots, and live UniProt, AlphaFold DB, and RCSB lookups. Also ships a point-and-click Protein Lab web UI (and a persistent run registry) so students and wet-lab biologists can get the same results without any client setup.
    31
    MIT
  • A
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    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
  • A
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    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
  • A
    license
    Not graded
    quality
    B
    maintenance
    Enables searching ENA's public sequencing data by organism, study, platform, country or date, retrieving FASTQ/BAM download URLs and checksums, and discovering available result types and fields.
    454 npm
    MIT
  • A
    license
    Not graded
    quality
    B
    maintenance
    Enables querying gene expression experiments, brain region structure ontologies, and in-situ hybridization datasets from the Allen Institute's Brain Atlas public API.
    260 npm
    MIT
  • A
    license
    Not graded
    quality
    B
    maintenance
    Enables AI agents to search public cancer genomics studies (TCGA, CPTAC, MSK, and more), fetch full details for individual studies, resolve gene symbols to Entrez ids, and list cancer types. Works keylessly against open cBioPortal data over a hosted MCP endpoint, a local stdio server, or plain HTTP.
    414 npm
    MIT
  • A
    license
    Not graded
    quality
    C
    maintenance
    An MCP server that enables scRNA-Seq analysis through natural language, providing tools for data preprocessing, clustering, and biological visualization. It supports both predefined function execution and a flexible code mode powered by a Jupyter backend for automated single-cell transcriptomics workflows.
    16
    BSD 3-Clause
  • A
    license
    Not graded
    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
  • 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
  • A
    license
    A
    quality
    A
    maintenance
    Enables language models to search biomedical literature, fetch sequences, and follow links across Entrez databases through eleven read-only tools wrapping the nine NCBI Entrez E-utilities. It handles URL building, pacing, redirects, response caps, and API-key redaction so queries can be answered without a browser or scraping.
    11
    MIT
  • A
    license
    A
    quality
    B
    maintenance
    Enables DNA sequence analysis and variant effect prediction using Evo2-7B via MCP tools, providing forward inference, likelihood scoring, and batch variant comparison through natural language.
    5
    Apache 2.0
  • A
    license
    A
    quality
    A
    maintenance
    Guides researchers, including those new to BPP, from raw sequence data to a validated control file that has passed a short test run. Wraps BPP command-line tools without running long analyses itself.
    16
    AGPL 3.0
  • A
    license
    A
    quality
    C
    maintenance
    Provides read-only access to the ProPaths verified protein interactome, letting AI agents search proteins, retrieve mechanistic interaction details, and explore pathway ontology through MCP tools, resources, and prompts.
    11
    11 PyPI
    MIT
  • A
    license
    A
    quality
    D
    maintenance
    MCP server that exposes the UniProt REST API to LLM clients, enabling search and retrieval of protein data via tools like search_uniprotkb, get_entry, and map_ids.
    7
    MIT
  • 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
  • A
    license
    A
    quality
    B
    maintenance
    Enables MCP clients to annotate and classify single human genetic variants in any notation, returning an auditable points-based ACMG verdict with its criteria, gnomAD frequencies, in-silico predictors, ClinVar data, and per-transcript consequences. It is read-only, requires no account or API key, and keeps answers compact while linking back to the source.
    6
    MIT
  • A
    license
    A
    quality
    A
    maintenance
    MCP server for the STRING protein–protein interaction database, hosted by STRING at mcp.string-db.org. Adapted for LLM grounding: responses are size-limited and include metadata and notes on interpretation and next steps. Tools cover identifier resolution, interaction networks and evidence, functional and PPI enrichment, and sequence similarity search.
    17
    8
    MIT
  • A
    license
    A
    quality
    A
    maintenance
    MCP server that provides tools for querying the Human Phenotype Ontology (HPO) including term lookup, hierarchy exploration, cross-ontology mappings, and gene-phenotype-disease associations, all grounded in a local SQLite database for fast offline lookups.
    17
    1
    MIT
  • A
    license
    A
    quality
    B
    maintenance
    MCP server offering verified bioinformatics tools for sequence utilities and statistics, backed by BioPython/scipy. Enables AI agents to perform accurate GC content, translation, ORF finding, motif scanning, and statistical tests through natural language.
    11
    MIT
  • A
    license
    A
    quality
    C
    maintenance
    Enables LLM agents to search EMDB cryo-EM maps, look up UniProt proteins, compute ESM-2 sequence embeddings, retrieve cryo-EM maps from a protein sequence via a two-tower model, and search GEO DNA-methylation arrays, all through typed tools with structured output. Ships with a 40-question evaluation harness that runs Claude as the MCP client.
    3
    MIT
  • A
    license
    A
    quality
    C
    maintenance
    Enables users to search multiple public life-science data repositories (GEO, ENA, CELLxGENE, PRIDE, DataCite) with a single query, returning a unified ranked list of datasets with ontology-expanded terms and per-source error reporting.
    3
    MIT
  • A
    license
    A
    quality
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    maintenance
    Enables querying the EMBL-EBI catalog of published polygenic scores through read-only tools that search scores, traits, publications, performance metrics, sample sets, cohorts, and releases, and that trace GWAS studies and resolve ontology and ancestry identifiers. It also lists and downloads the associated scoring-file and metadata files from the catalog's FTP site.
    24
    1
    Apache 2.0