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.1613 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

io.github.rcsb/rcsb-mcpofficial
AlicenseAqualityAmaintenanceEnables discovery, inspection, and cross-referencing of Protein Data Bank structures through three RCSB APIs: search, data, and sequence coordinates.3611MIT
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.28138 PyPI10Apache 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.3443Apache 2.0
CEDAR MCP Serverofficial
AlicenseAqualityBmaintenanceEnables interaction with the CEDAR metadata repository, including fetching templates, searching BioPortal ontology terms, and managing template instances.831 PyPIMIT
GeneBe MCPofficial
AlicenseAqualityBmaintenanceEnables 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.6MIT
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.2323 PyPI3MIT
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.5606Apache 2.0
millimap-mcpofficial
AlicenseAqualityDmaintenanceEnables 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.123 npmMIT- AlicenseAqualityBmaintenanceA stateless, deterministic Bio-Robotics Core Engine converting biological data (UniProt API) to G-code.6MIT
- AlicenseBqualityAmaintenanceAn 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.5231Apache 2.0
- AlicenseBqualityCmaintenanceAllows to retrieve information about an AnnData object via MCP using the read_lazy function from anndata.339 PyPI7MIT
- 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.101,804 npm10Apache 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.181MIT
- AlicenseBqualityBmaintenanceEnables 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.13MIT
- 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
- AlicenseAqualityCmaintenanceConverts 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.131Apache 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.71,881 npm99Apache 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
- AlicenseAqualityBmaintenanceMCP server for polygenic risk score analysis, wrapping just-prs to enable catalog search, PRS computation, VCF normalization, percentile and risk estimation, and quality assessment.201MIT
MCP ConnectorsBrowse all →
Query STRING interactions, enrichment, annotations, homology, and PPI networks.
Pharmacogenomics for AI agents: cited drug–gene, gene and rsID lookups plus a medication screen.
ACMG/AMP germline variant classification, gene profiles, disease associations and literature.
Diagnoses, drugs & lab codes: ICD-11, LOINC, RxNorm, MeSH, ATC, CID-10. 33 tools, MIT.
Due diligence on life-science claims: omics, trials, gene therapy. Dimension by dimension.
Sovereign intelligence dossiers, daily briefings, RAG search, knowledge graph, codon optimizer.
Run protein folding, docking, design and sequence analysis tools, and read their results.
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.
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.
Ancestry allele frequencies, LoF constraint, variant lists, and coverage from gnomAD, with ClinVar.
Search GBIF species taxonomy, occurrence records, datasets, and publishers.
Link compounds to protein targets, rank bioactivity, and look up drug mechanisms and indications.
Look up genes, sequences, variants, homologs, and cross-database xrefs from Ensembl REST.
Resolve WoRMS marine species names; fetch classifications, synonyms, distributions, traits, and IDs.
Search InterPro entries, map domains onto proteins and PDB structures, and scan raw sequences.
Biomedical data: compounds, drug info, and molecular targets
Find pharmacogenomics guidelines, translate diplotypes, and retrieve prescribing recommendations.
Protein research over UniProtKB: search by function, fetch curated records, map IDs, proteomes.
PomBase MCP — the fission yeast (Schizosaccharomyces pombe) model-organism database.