A
licenseA
qualityA
maintenanceA bridge connecting AI agents to NCBI's PubMed database through the Model Context Protocol, enabling seamless searching, retrieval, and analysis of biomedical literature and data.
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"How to find or generate YouTube video transcripts" matching MCP servers:
- AlicenseAqualityAmaintenanceEnables 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.11MIT
igvf-portal-mcpofficial
Alicense-qualityBmaintenanceEnables AI agents to search, filter, download files, and generate reports from the IGVF Data Portal using natural language commands.1MIT- Alicense-qualityDmaintenanceEnables AI assistants to generate publication-quality bioinformatics visualizations (volcano plots, PCA, heatmaps, etc.) directly from raw biological data.MIT
- Alicense-qualityDmaintenanceSearches UniProt by protein name to find accession numbers and retrieves detailed protein structure information from AlphaFold, including direct links to 3D structural predictions.3MIT
- FlicenseAqualityDmaintenanceEnables AI assistants to clean PDB structures and run initial-stage energy relaxation for biomolecular modeling. It provides a structured workflow for preparing structures before production molecular dynamics or coarse-graining pipelines.9
- AlicenseAqualityDmaintenanceA 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.88MIT
- AlicenseAqualityDmaintenanceEnables AI assistants to query the Ubergraph biomedical ontology SPARQL endpoint with tools for custom SPARQL queries, term lookup, search, and hierarchy traversal.4MIT
- FlicenseAqualityDmaintenanceProvides access to EMBL-EBI bioinformatics data including InterPro domains, Pfam families, protein features, and taxonomy through a unified tool.11
- AlicenseAqualityAmaintenanceProvides LLMs with structured access to critical biomedical databases including PubTator3 (PubMed/PMC), ClinicalTrials.gov, and MyVariant.info through the Model Context Protocol.35591MIT
- AlicenseAqualityDmaintenanceEnables bioinformatics analysis through natural language conversations with Claude Desktop, automatically generating and executing Python scripts to produce HTML reports and visualizations.3139MIT
- AlicenseAqualityDmaintenanceA high-performance MCP server that gives LLMs access to 25 biomedical tools federated across 50+ upstream APIs for genes, variants, drugs, diseases, literature, clinical trials, and structural biology.25672MIT
- FlicenseAqualityDmaintenanceLeverages 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.44
PDBe MCP Serversofficial
AlicenseBqualityAmaintenanceProvides seamless access to the Protein Data Bank in Europe (PDBe) API and search capabilities, enabling AI clients to query protein structures, perform advanced searches, and retrieve structural biology data.3337Apache 2.0- AlicenseBqualityFmaintenanceProvides standardized access to aging and longevity research data from the OpenGenes database, enabling AI assistants to query comprehensive biomedical datasets through SQL and structured interfaces.320MIT
- AlicenseBqualityDmaintenanceProvides seamless access to UniProtKB protein database, enabling queries for protein entries, sequences, Gene Ontology annotations, full-text search, and ID mapping across 200+ database types.52MIT
- FlicenseBqualityDmaintenanceProvides programmatic access to AlphaFold protein structure predictions and UniProt data, enabling users to retrieve protein structures, summaries, and annotations through natural language.3
- AlicenseBqualityDmaintenanceEnables AI assistants to access protein information directly from UniProt, allowing retrieval of protein names, functions, sequences, and organism data by accession number.214MIT
- AlicenseBqualityDmaintenanceA 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.113BSD 3-Clause