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MCP servers tagged bioinformatics
167 live MCP servers tagged "bioinformatics", ranked by trust score. Tags come from package metadata and repository topics, so this list covers servers across every category that work with bioinformatics.
Hpo Link
MCP server for the Human Phenotype Ontology (HPO): phenotype term lookup, the is_a hierarchy, cross-ontology mapping, and gene–phenotype–disease associations from HPO and HPOA.
Awesome Bio Agents
A curated collection of AI agents, harnesses, MCP servers, skills, tools and benchmarks for biological research.
Heuris BioMCP
BioMCP - Comprehensive MCP server for bioinformatics and life sciences
SDK Typescript
🚀 Build efficient applications with the MCP SDK for TypeScript, offering optimized performance, real-time communication, and robust session management.
STAMP
Solid Tumor Associative Modeling in Pathology
Helix
A declarative DSL and compiler for reproducible gene-editing design — with LLM agents and an MCP server so any AI agent can drive it safely.
Vcf MCP
MCP Connector for VCF Genetic Data File(s). Single, multiple, comparison, data setting, etc.
Awesome Scientific AI Tools
Discover AI tools, MCP servers, and agent skills for scientific research across literature, data, writing, and lab work
Lifesciences Research
AI Agent wrappers for Life Sciences APIs (Open Targets, ChEMBL, UniProt). Accelerating drug discovery with Model Context Protocol (MCP) and FastMCP.
PDBe MCP Servers
PDBe MCP Servers integrate Protein Data Bank Europe resources with LLMs via Model Context Protocol. Provides seamless access to protein structure data through API tools and graph…
Posebusters MCP Server
Unofficial MCP server for PoseBusters – validate molecular poses via HTTP or Spaces using the Model Context Protocol (MCP).
Biothings Typed Client
Client that provides typed definitions to biothings client
SEOSiri-Official/biorobotics
code coordinates using the Model Context Protocol. 🐍 🏠 🍎 🪟 🐧
GrEBI
HPC aggregation pipeline and API/MCP server for LLM-mediated biomedical data integration
Nf Runinsights
Nextflow plugin for cross-run benchmarking. Records per-process metrics for every run into a local or shared history store, compares runs against their own history, and flags regr…
LibreGene
An open-source, agent-ready plasmid editor.
Stringdb Link
MCP server for STRING v12: protein–protein association networks, interaction partners, and functional enrichment analysis — as typed tools for LLM agents.
Fgbio MCP Servers
MCP Wrappers for fgbio Tools
Mgi Link
MCP server for MGI (Mouse Genome Informatics): mouse gene, allele, mutation and phenotype data — the MGI marker page as structured tools, served from a local SQLite index.
Oncotarget Luad
Scientific MVP for LUAD target prioritization using knowledge graphs, GraphSAGE, and GraphRAG.
Mygene MCP
MCP server for MyGene.info API
Mydisease MCP
MCP server for MyDisease.info API
Gtex Link
MCP server for the GTEx Portal: tissue-specific gene expression — median and per-sample TPM, top expressed genes per tissue, and gene/transcript annotation — as typed tools for LL…
Genereviews Link
MCP server for GeneReviews: the expert-authored, peer-reviewed gene–disease chapters on NCBI Bookshelf, served as a searchable corpus of individually citable passages.
Autopvs1 Link
MCP server for AutoPVS1: automated ACMG PVS1 loss-of-function evidence for sequence variants and copy-number variants — variant interpretation as typed tools for LLM agents.
Biomedical Terminology Service
The BioMedical Terminology Service (BTS) is a self-hosted platform that provides one API for searching, traversing, mapping and semantically comparing concepts across major biomed…
Litvar Link
MCP server for NCBI LitVar2: search the biomedical literature by genetic variant — the index linking variants to the publications that mention them, as typed tools for LLM agents.
Pubtator Link
MCP server for NCBI PubTator3: biomedical literature search with gene, variant, disease and chemical entity annotation — returns compact, citable passages instead of raw BioC.
Gnomad Link
MCP server for gnomAD (Genome Aggregation Database): variant allele frequencies, gene constraint, coverage, structural and mitochondrial variants, and liftover — as typed tools fo…
Mavedb Link
MCP server for MaveDB: quantitative variant-effect scores from Multiplexed Assays of Variant Effect (MAVE) and deep mutational scanning — functional evidence as typed tools for LL…
Mondo Link
MCP server for the Mondo Disease Ontology: disease term lookup, the is_a hierarchy, and cross-ontology mapping across OMIM, Orphanet, DOID, NCIT, UMLS and MeSH.
Genepattern MCP
MCP server that lets AI assistants (Claude, Cursor, Copilot) run GenePattern bioinformatics modules, manage cloud jobs, and access genomic data — all through natural language.
Mutcompute MCP
MutCompute MCP server for protein mutation effect prediction
Boltzgen MCP
BoltzGen MCP server for protein binder design
Bindcraft MCP
BindCraft MCP server for de novo protein binder design
Boltz MCP
Boltz2 MCP server for protein structure and affinity prediction
Claude Code Biology Research
?? A comprehensive guide to using Claude Code as an AI-powered assistant for computational biology, bioinformatics, and biomedical research
Agentic Genomics
Connect whole-genome sequencing data to AI coding assistants via the Model Context Protocol (MCP). Setup guides for GeneChat-MCP, OpenCRAVAT-MCP, and Pomera across Antigravity, Co…
Netmhc2pan MCP
NetMHCIIpan MCP server for MHC Class II binding prediction
Prottrans MCP
ProtTrans MCP server for protein embeddings and fitness modeling
Alphafold3 MCP
AlphaFold3 MCP server for protein structure prediction, supporting batch prediction
Genefoundry
A modular registry for trustworthy, evidence-based genomic analysis powered by Model Context Protocols (MCPs). Bridging AI and clinical genomics with traceable, validated data ret…
Proteinmpnn MCP
ProteinMPNN MCP server for protein sequence design (inverse folding)
Ev Onehot MCP
EV+Onehot MCP server for protein fitness prediction combining evolutionary coupling and one-hot encoding
Rfdiffusion2 MCP
RFdiffusion2 MCP server for protein structure generation (backbone)
Oncora
Oncora — A Reproducible, Uncertainty-Aware Agentic Reasoning Platform for Oncology Drug Discovery (Rust-native, on-prem, MCP)
Flowproof MCP
Run reproducible bioinformatics pipelines from an AI assistant over MCP, with verifiable provenance
Chilecule
Agentic drug discovery workflows on fully open-source tooling: RDKit, AutoDock Vina/smina, fpocket, ChEMBL. MCP tool servers + Claude agents, with a retrospective validation harne…
Litmuz Agent
Claim-level verification for life-sciences research agents: honest, auditable, per-claim traffic-light verdicts against the primary literature and genomic reference data. MCP-nati…
Mychem MCP
MCP server for MyChem.info API