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 →
- AlicenseAqualityBmaintenance▎ Provides 32 tools for plant-genomics locus lookup across 11 free public backends (Ensembl Plants, Phytozome, UniProtKB, Europe PMC, QuickGO, NCBI BLAST, Gramene, KEGG, STRING-DB, ATTED-II, BAR). Takes a TAIR-style locus plus optional organism and returns gene metadata, functional/pathway annotation, interactions, co-expression, and literature — in single-locus, batch, and cross-source synthesis.Last updated3232MIT

Noctua MCP Serverofficial
AlicenseAqualityBmaintenanceEnables 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
millimap-mcpofficial
AlicenseAqualityCmaintenanceEnables Claude Desktop to read and drive analyses on the active MilliMap session, including datasets, clusters, annotations, and markers.Last updated12MIT
WormBase MCP Serverofficial
AlicenseAqualityCmaintenanceEnables 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 updated121MIT- AlicenseAqualityCmaintenanceEnables 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 updated16159MIT
- AlicenseBqualityBmaintenanceIntelligent Genomic Data Server Provides high-quality gene information queries, homologous gene analysis, and evolutionary research functions via the MCP protocol.Last updated62MIT
- AlicenseAqualityCmaintenanceConverts natural language queries into Cypher queries against the NASA GeneLab Knowledge Graph, enabling AI-assisted analysis of spaceflight experiments and their biological effects.Last updated122BSD 3-Clause
- AlicenseAqualityBmaintenanceEnables gene set enrichment analysis using the Enrichr API across hundreds of gene set libraries including Gene Ontology, pathways, diseases, tissues, drugs, and transcription factors. Returns only statistically significant results for interpretation.Last updated28014MIT
- AlicenseAqualityAmaintenanceProvides LLMs with structured access to critical biomedical databases including PubTator3 (PubMed/PMC), ClinicalTrials.gov, and MyVariant.info through the Model Context Protocol.Last updated35517MIT
- AlicenseBqualityBmaintenanceProvides comprehensive BioPython capabilities for biological sequence analysis, alignment, database access (GenBank, UniProt, PubMed), protein structure analysis, and phylogenetics through a Model Context Protocol interface for AI-assisted bioinformatics workflows.Last updated322MIT
- AlicenseBqualityCmaintenanceProvides 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 updated9ISC
- AlicenseAqualityCmaintenanceA 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.Last updated87MIT
- AlicenseBqualityCmaintenanceProvides 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.Last updated318MIT
- AlicenseAqualityCmaintenanceEnables AI agents to conversationally interact with genomics research networks for data analysis and discovery across multiple Omics AI Explorer platforms. It provides tools for exploring data collections, examining table schemas, and executing SQL queries against datasets like Viral AI and Neuroscience AI.Last updated61MIT
- AlicenseBqualityCmaintenanceEnables AI assistants to access protein information directly from UniProt, allowing retrieval of protein names, functions, sequences, and organism data by accession number.Last updated211MIT
- AlicenseBqualityDmaintenanceSearch PubMed for articles matching the query.Last updated163MIT
- AlicenseBqualityCmaintenanceProvides seamless access to UniProtKB protein data, enabling querying of protein entries, sequences, Gene Ontology annotations, and ID mappings through a typed, resilient interface.Last updated5MIT
- AlicenseBqualityCmaintenanceProvides 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
- AlicenseBqualityCmaintenanceEnables AI-powered genomic variant analysis including variant impact prediction, regulatory element discovery, and batch variant scoring. Currently operates in mock mode as a proof-of-concept awaiting the public release of Google DeepMind's AlphaGenome API.Last updated20152MIT
- AlicenseBqualityBmaintenanceProvides a programmatic interface to the Genome Aggregation Database (gnomAD) API across versions v2.1.1, v3.1.2, and v4.1.0. It enables users to query gene metadata, variant information, population frequencies, and ClinVar data through a unified schema.Last updated125Apache 2.0
- AlicenseAqualityCmaintenanceA Model Context Protocol (MCP) server for interacting with Gen3 data commons, with GraphQL query validation to reduce hallucinations.Last updated54MIT
- AlicenseBqualityDmaintenanceEnables 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
- AlicenseBqualityCmaintenanceEnables 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
- AlicenseBqualityCmaintenanceProvides 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
- AlicenseBqualityCmaintenanceServer to search PubMed (PubMed is a free, online database that allows users to search for biomedical and life sciences literature). I have created on a day MCP came out but was on vacation, I saw someone post similar server in your DB, but figured to post mine.Last updated147MIT
- AlicenseAqualityAmaintenanceNatural language-driven spatial transcriptomics analysis via MCP. Integrates 60+ methods for preprocessing, visualization, spatial statistics, cell communication, deconvolution, and trajectory analysis.Last updated2038MIT
- AlicenseBqualityCmaintenanceA 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
- AlicenseAqualityCmaintenanceAn MCP server that provides tools for searching and fetching protein data from the UniProt database using the unipressed library.Last updated2MIT
- AlicenseAqualityCmaintenanceA 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.Last updated108JavaScriptMIT
- AlicenseAqualityBmaintenanceProvides an MCP interface to the ROBOT command-line tool for OWL ontology editing, enabling operations like merging, reasoning, and conversion via natural language.Last updated261BSD 2-Clause "Simplified"
MCP ConnectorsBrowse all →
A unified biomedical graph database that integrates 50+ primary data sources — genes, proteins, compounds, diseases, pathways, and clinical data — into a single queryable graph with billions of cross-reference edges. Its native MCP server gives LLMs direct access to structured, authoritative biomedical data, complementing their reasoning with reliable identifiers and up-to-date database content.
Search GBIF species taxonomy, occurrence records, datasets, and publishers.
Biotech rNPV/PoS engine for AI agents. Signed exports, evidence register, asset landscape.
- GtexA
GTEx — Genotype-Tissue Expression human gene-expression atlas
STRING protein-protein interaction networks across ~12k organisms
Monarch biomedical knowledge graph — diseases, phenotypes, genes, variants
MyGene.info — gene annotation joining NCBI/Ensembl/UniProt/KEGG/OMIM
Bioregistry — meta-registry of biomedical identifier prefixes
Ensembl REST — vertebrate genomes, sequences, comparative genomics, variation
AI orchestration for computational chemistry and HPC workflows.
Gencove consumer genomics: profile, kit status, ancestry, PRS, raw data. Requires Gencove auth.
PatSnap Biology Modality MCP server — access biological sequences, modification records, and antibody-antigen interactions across 200M+ patents.
Chemical molecular intelligence platform covering compound search, structure analysis, physicochemical property retrieval, and molecular interaction profiling.