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 →
- 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.1622 npm12MIT
- AlicenseAqualityAmaintenanceEnables agents to search a public PubMed-derived corpus by natural language or identifiers and to retrieve publication details while traversing bounded citation and semantic literature graphs.7Apache 2.0
- AlicenseAqualityAmaintenanceAn MCP server that interfaces with Gigwa for genotyping data import, analysis, and audit, enabling users to perform complex workflows through natural language commands.835Apache 2.0
- AlicenseAqualityAmaintenanceMCP 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.6177MIT

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.364MIT
openreadoutofficial
AlicenseAqualityAmaintenanceReads raw lab-instrument files (microscopy, mass spectrometry, chromatography, flow cytometry, NMR, electrophysiology, spectroscopy, plate readers, qPCR) without vendor software, returning metadata, images, spectra and traces as JSON. It also checks files for damage, runs common analyses, and exports to open formats such as OME-TIFF, OME-Zarr, mzML, Parquet and NWB.15Apache 2.0
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.3340Apache 2.0
CEDAR MCP Serverofficial
AlicenseAqualityAmaintenanceEnables interaction with the CEDAR metadata repository, including fetching templates, searching BioPortal ontology terms, and managing template instances.8MIT
Genomics MCPofficial
AlicenseBqualityAmaintenanceRetrieve genomic data from EGA, ENA, ENCODE, GEO and NCBI, read bounded regions from indexed BAM/CRAM, VCF and bigWig files, and query source-attributed reference evidence. Runs locally with 23 MCP tools. MIT-licensed; research use.233MIT
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.18BSD 3-Clause
reactome-mcpofficial
AlicenseBqualityCmaintenanceEnables AI assistants to search, browse, analyze, and export biological pathway data from Reactome through natural language.56443 npm6Apache 2.0
millimap-mcpofficial
AlicenseAqualityCmaintenanceEnables Claude Desktop to read and drive analyses on the active MilliMap session, including datasets, clusters, annotations, and markers.12MIT
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.1210 npmMIT- AlicenseAqualityAmaintenanceA stateless, deterministic Bio-Robotics Core Engine converting biological data (UniProt API) to G-code.6MIT
- AlicenseBqualityCmaintenanceAn 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.5230Apache 2.0
- AlicenseBqualityCmaintenanceAllows to retrieve information about an AnnData object via MCP using the read_lazy function from anndata.37MIT
- AlicenseAqualityAmaintenanceEnables AI agents and applications to search, retrieve, and analyze chemical compounds, substances, and bioassays from PubChem's vast chemical information database through comprehensive tools for chemical research and discovery.10788 npm9Apache 2.0
- AlicenseAqualityDmaintenanceEnables AI-assisted molecular biology experiment design with tools for qPCR primer design, cloning strategy optimization, TaqMan probe design, and multiplex compatibility analysis.61MIT
- 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.15MIT
- AlicenseBqualityDmaintenanceSearch PubMed for articles matching the query.170MIT
- AlicenseBqualityCmaintenanceEnables AI coding agents to search academic papers, resolve biomedical entities, mine relations, and traverse citation graphs using Semantic Scholar and PubTator3, with local caching for reproducibility.11MIT
- AlicenseAqualityDmaintenanceEnables AI assistants to rapidly gather and synthesize structural, chemical, conservation, and literature data about protein binding pockets for drug-target triage. Useful as a reconnaissance step before computational binder design.81MIT
- AlicenseAqualityAmaintenanceProvides local DNA/RNA sequence analysis tools (composition, reverse complement, translation, ORF enumeration, motif scanning) via MCP for agent workflows.5MIT
- 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.12MIT
- AlicenseBqualityBmaintenanceEnables 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.1330 PyPIMIT
- AlicenseAqualityBmaintenanceEnables researchers to query public ENA and BioSamples genomics data in plain English through any MCP client, including counting records, searching samples, retrieving sample details, and checking metadata quality against project requirements.4MIT
- AlicenseAqualityBmaintenanceConverts 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.20MIT
- AlicenseAqualityCmaintenanceMCP server exposing REINVENT4 generative molecular-design operations as validated, LLM-callable tools for drug discovery, including sampling, transfer learning, reinforcement learning, and molecular analysis.13Apache 2.0
- AlicenseAqualityAmaintenanceEmpowers AI agents with direct access to the official ClinicalTrials.gov database, enabling programmatic searching, retrieval, and analysis of clinical study data through a Model Context Protocol interface.71,180 npm97Apache 2.0
- 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.9MIT
MCP ConnectorsBrowse all →
Diagnoses, drugs & lab codes: ICD-11, LOINC, RxNorm, MeSH, ATC, CID-10. 33 tools, MIT.
Official STRING database MCP server. Query for protein-protein interactions, enrichment, annotations, homology, and PPI networks.
Run protein folding, docking, design and sequence analysis tools, and read their results.
Sovereign intelligence dossiers, daily briefings, RAG search, knowledge graph, codon optimizer.
Read-only MCP connector for The Dose Guy source-linked peptide and compound database. Search 260+ compounds, compare vendors and prices, inspect ranking evidence, and retrieve canonical page links. No authentication required.
Due diligence on life-science claims: omics, trials, gene therapy. Dimension by dimension.
Bioinformatics MCP for genomic variant interpretation, gene-disease evidence and literature.
Search biomedical papers, inspect publication records, and traverse citation or semantic graphs.
Official answers about Helena Bioinformatics and its products, with citations to public sources.
Look up genes, sequences, variants, homologs, and cross-database xrefs from Ensembl REST.
Biomedical data: compounds, drug info, and molecular targets
Look up allele frequencies by ancestry, gene constraint, variants, and coverage over gnomAD.
Link compounds to protein targets, rank bioactivity, and look up drug mechanisms and indications.
Collaborative BrAPI v2.1 MCP workspace — studies, germplasm, genotypes across Breedbase, T3, more.
BioBricks: the site's own MCP server — dataset, enquiry (enquiry = a human handoff, not a...
Protein research over UniProtKB — search by function, fetch curated records, map IDs, proteomes.
Cancer gene co-occurrence and exclusivity in tumour cohorts, with confound controls and exact tests.
Search GBIF species taxonomy, occurrence records, datasets, and publishers.
Cited gene, variant (rsID) and CPIC drug–gene lookups for AI agents. Read-only, no key.
HLA nomenclature and match checks against a pinned IPD-IMGT/HLA release. No patient identifiers.