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licenseA
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maintenanceA stateless, deterministic Bio-Robotics Core Engine converting biological data (UniProt API) to G-code.
Last updated
30
6
MIT
Bioinformatics
Tools for computational analysis of biological data, including genomics, proteomics, and other molecular biology data. Enables access to bioinformatics pipelines, algorithms, and databases.
MCP ServersBrowse all →
Noctua MCP Serverofficial
AlicenseAqualityCmaintenanceEnables 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.Last updated18BSD 3-Clause- AlicenseAqualityCmaintenanceAn MCP server that provides standardized access to biomedical knowledge bases and resources, enabling AI systems to retrieve verified information from sources like bioRxiv, EuropePMC, and various protein/gene databases.Last updated5228Apache 2.0
- AlicenseAqualityDmaintenanceEnables AI-driven pharmacogenomic analysis by querying structured genetic variant, drug response, and disease risk data. Supports natural language questions about medications, traits, and health risks based on user genome data, with privacy-first local execution.Last updated163711MIT
WormBase MCP Serverofficial
AlicenseAqualityDmaintenanceEnables querying the WormBase database for C. elegans and nematode genomics data, including gene information, protein sequences, phenotypes, interactions, and expression patterns through natural language.Last updated1219MIT
millimap-mcpofficial
AlicenseAqualityDmaintenanceEnables Claude Desktop to read and drive analyses on the active MilliMap session, including datasets, clusters, annotations, and markers.Last updated12MIT
CEDAR MCP Serverofficial
AlicenseAqualityCmaintenanceEnables interaction with the CEDAR metadata repository, including fetching templates, searching BioPortal ontology terms, and managing template instances.Last updated8MIT
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.Last updated3336Apache 2.0
io.github.rcsb/rcsb-mcpofficial
AlicenseAqualityBmaintenanceEnables discovery, inspection, and cross-referencing of Protein Data Bank structures through three RCSB APIs: search, data, and sequence coordinates.Last updated363MIT- 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.Last updated11MIT
- 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.Last updated52MIT
- AlicenseBqualityDmaintenanceProvides access to the STRING protein-protein interaction database for mapping identifiers, retrieving interaction networks, and performing functional enrichment analysis. It enables users to explore protein partners, pathways, and cross-species homology through natural language interactions.Last updated91ISC
- AlicenseBqualityFmaintenanceEnables molecular design and simulation through 45 chemistry tools including pKa calculations, geometry optimization, conformer searches, docking, protein cofolding, and ADMET predictions powered by Rowan's computational chemistry platform.Last updated4123MIT
- AlicenseAqualityDmaintenanceA Model Context Protocol (MCP) server for interacting with Gen3 data commons, with GraphQL query validation to reduce hallucinations.Last updated54MIT
- AlicenseAqualityCmaintenanceEnables variant annotation and effect prediction using the Ensembl VEP API, with support for batch and single queries.Last updated91MIT
- AlicenseAqualityDmaintenanceEnables natural language control of UCSF ChimeraX for protein structure visualization, editing, and analysis through MCP clients.Last updated393MIT
- AlicenseAqualityAmaintenanceAn 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.Last updated15MIT
- AlicenseBqualityDmaintenanceEnables AI assistants to access protein information directly from UniProt, allowing retrieval of protein names, functions, sequences, and organism data by accession number.Last updated213MIT
- 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.Last updated113BSD 3-Clause
- AlicenseAqualityAmaintenanceGrounds gene-nomenclature work in the HUGO Gene Nomenclature Committee (HGNC) dataset, enabling resolution of gene symbols and IDs to canonical HGNC identifiers, plus cross-references and batch operations.Last updated9MIT
- AlicenseAqualityCmaintenanceProvides direct SQL access to a locally hosted Reactome database, enabling schema discovery, guarded read-only queries, and ergonomic helpers over the full relational schema.Last updated9MIT
- AlicenseAqualityAmaintenanceAn MCP server that provides mouse genetics data from Mouse Genome Informatics (MGI), enabling LLM agents to query markers, mutations, alleles, phenotypes, and disease models.Last updated131MIT
- AlicenseAqualityDmaintenanceEnables AI assistants to query the Ubergraph biomedical ontology SPARQL endpoint with tools for custom SPARQL queries, term lookup, search, and hierarchy traversal.Last updated4MIT
- AlicenseBqualityDmaintenanceEnables searching, retrieving, and downloading protein structure data from the RCSB Protein Data Bank. Supports intelligent protein structure search, comprehensive data retrieval, and multiple file format downloads for bioinformatics research.Last updated3MIT
- AlicenseBqualityDmaintenanceMCP server providing access to the BERtron API for aggregating genomic and environmental data from multiple BER data sources, enabling geospatial search and health checks.Last updated83BSD 3-Clause
- AlicenseBqualityDmaintenanceProvides access to the Ensembl genomics REST API with 30+ tools for genomic data including gene lookup, sequence retrieval, genetic variants, cross-species homology, phenotypes, and regulatory features.Last updated25ISC
- AlicenseAqualityAmaintenanceMCP 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.Last updated17MIT
- AlicenseAqualityDmaintenanceEnables the generation, mutation, and evolution of DNA and protein sequences using various evolutionary models and phylogenetic algorithms. It supports realistic next-generation sequencing read simulation and population-level evolutionary tracking for bioinformatics research and testing.Last updated6BSD 2-Clause "Simplified"
- AlicenseBqualityDmaintenanceProvides comprehensive access to the UCSC Genome Browser API, enabling queries of genomic data, DNA sequences, gene annotations, variants, and metadata across multiple species and assemblies.Last updated126MIT
- AlicenseAqualityAmaintenanceMCP server that provides tools to query harmonized gene-disease validity data from the Gene Curation Coalition, supporting consensus and conflict detection for gene-disease assertions.Last updated12MIT
MCP ConnectorsBrowse all →
RCSB PDB MCP — experimentally determined macromolecular structures.
Monarch biomedical knowledge graph — diseases, phenotypes, genes, variants
STRING protein-protein interaction networks across ~12k organisms
Ensembl REST — vertebrate genomes, sequences, comparative genomics, variation
Bioregistry — meta-registry of biomedical identifier prefixes
Search GBIF species taxonomy, occurrence records, datasets, and publishers.
GTEx — Genotype-Tissue Expression human gene-expression atlas
MyGene.info — gene annotation joining NCBI/Ensembl/UniProt/KEGG/OMIM
Hosted DNA language models: promoter, splice, enhancer, chromatin, expression, annotation
Query STRING interactions, enrichment, annotations, homology, and PPI networks.
Look up genes, fetch sequences, predict variant consequences, find orthologs and xrefs via Ensembl.
Hosted DNA/RNA/protein tools: primers, oligos, PCR, cloning, CRISPR, alignment, batch & pipelines.
Canine genomics for agents: breed allele frequencies, AI pathogenicity + OMIA clinical disease layer
UniProt MCP — protein sequence + function database.
Biotech intelligence for AI agents: drugs, targets, diagnostics, PoS estimates, and writeups.