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 npm11MIT
- 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

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.363MIT
PDBe MCP Serversofficial
AlicenseBqualityBmaintenanceProvides 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.3339Apache 2.0
CEDAR MCP Serverofficial
AlicenseAqualityAmaintenanceEnables interaction with the CEDAR metadata repository, including fetching templates, searching BioPortal ontology terms, and managing template instances.8MIT
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
AlicenseBqualityBmaintenanceEnables AI assistants to search, browse, analyze, and export biological pathway data from Reactome through natural language.566Apache 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.124 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.5228Apache 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.10133 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.168MIT
- AlicenseBqualityAmaintenanceEnables 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
- AlicenseBqualityAmaintenanceEnables 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.1325 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
- AlicenseAqualityBmaintenanceEmpowers 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.7728 npm94Apache 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
- AlicenseAqualityAmaintenanceMCP 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
- AlicenseAqualityAmaintenanceProvides LLMs with structured access to critical biomedical databases including PubTator3 (PubMed/PMC), ClinicalTrials.gov, and MyVariant.info through the Model Context Protocol.35384 PyPI633MIT
- AlicenseAqualityDmaintenanceEnables bioinformatics analysis through natural language conversations with Claude Desktop, automatically generating and executing Python scripts to produce HTML reports and visualizations.38 npm9MIT
MCP ConnectorsBrowse all →
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.
Diagnoses, drugs & lab codes: ICD-11, SNOMED, LOINC, RxNorm, MeSH, ATC, CID-10. 33 tools, MIT.
Bioinformatics MCP for genomic variant interpretation, gene-disease evidence and literature.
Due diligence on life-science claims: omics, trials, gene therapy. Dimension by dimension.
Search biomedical papers, inspect publication records, and traverse citation or semantic graphs.
HLA nomenclature and match checks against a pinned IPD-IMGT/HLA release. No patient identifiers.
Protein research over UniProtKB — search by function, fetch curated records, map IDs, proteomes.
BioBricks: the site's own MCP server — dataset, enquiry (enquiry = a human handoff, not a...
Deterministic peptide reconstitution and dosing math, so assistants compute it instead of guessing.
PK serum simulation, reconstitution math and compound data for agents. Paid tools $0.01 via x402.
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.
Search GBIF species taxonomy, occurrence records, datasets, and publishers.
Look up genes, sequences, variants, homologs, and cross-database xrefs from Ensembl REST.
Official answers about Helena Bioinformatics and its products, with citations to public sources.
Search and resolve Naturepedia, Robbie's Razor, and GC-MRD-v2.0 canonical resources.
Query CAN-IMMUNE: cancer neoantigen mutations, peptides, cell lines, MHC-I binding. Read-only.
Query STRING interactions, enrichment, annotations, homology, and PPI networks.
Percent-triplet count, input discarded
PubMed id shape, value discarded