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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.
Spired Stab MCP
SPIRED-Stab MCP server for protein stability prediction
Ligandmpnn MCP
LigandMPNN MCP server for ligand-aware scaffold-based sequence generation (inverse folding)
Msa MCP
MSA MCP server for generating multiple sequence alignments using ColabFold
Protein Sol MCP
Protein-Sol MCP server for protein solubility prediction
Mmseqs2 MCP
MMseqs2 MCP server for sequence search, clustering, and MSA generation
Plmc MCP
PLMC MCP server for evolutionary coupling analysis for protein fitness prediction
Interpro MCP
MCP server for accessing InterPro data
Esm MCP
ESM MCP server for protein embedding and fitness modeling
Netmhcpan MCP
NetMHCpan MCP server for MHC Class I binding prediction
Alphafold2 MCP
AlphaFold2 MCP server for protein structure prediction, supporting complex and batch predictions
Esmfold MCP
ESMFold MCP server for protein structure prediction
Chai1 MCP
Chai-1 MCP server for protein structure prediction
Rosetta MCP
Rosetta MCP server for molecular modeling and protein design
Computase
Local, reproducible DNA and RNA sequence utilities for Python, with optional MCP access.
Bioinformatics MCP
🧬 A comprehensive MCP server for bioinformatics — 62 tools for genomics, transcriptomics, epigenetics & more. Connects AI agents to scanpy, biopython, squidpy, NCBI, UniProt, Ense…
ASAREE
A visual analytics platform for engineering, executing, and evaluating reproducible agentic AI teams using experimental design methods.
CellTypePilot
Agent-native, local-first plugin for auditable single-cell annotation with governed evidence, contrastive review, conservative abstention, and human-reviewed draft outputs.
NCBI Database MCP
To discover gene expression datasets by disease/condition and access comprehensive NCBI databases
Protein AI Research Assistant
AI-powered protein research assistant that helps find, verify, analyze, and predict protein information using curated biological data, retrieval, and local structure-prediction mo…
Proto Agent Workbench
Local AI workbench for auditable DNA design, real protein structures and governed biological materials. Python CLI, MCP and Windows desktop.
Codex Science
Codex-native life-sciences workflow pack with scientific skills, MCP connector catalog, and bilingual documentation.
Pd Discovery Platform
CrewAI multi-agent research platform with custom MCP servers for biomarker discovery and target identification in preclinical neuroscience
Ncbi Blast
MCP Server and Gradio app for performing NCBI Blast on a DNA sequence
Biometric Iot Bridge MCP
A sovereign, biometric-authenticated IoT security broker using the Model Context Protocol.
Bio Research Forge
Vendor-neutral Agent Plugins 1.0 and MCP suite for evidence-first life-science research, RNA figures, molecular tools, writing, and review.
OpentargetMCP
Powerful Model Context Protocol (MCP) server for therapeutic discovery and drug repurposing using the Open Targets Platform GraphQL API.
Fastx MCP
MCP server for FASTA/FASTQ manipulation
wjgoarxiv/pymol-mcp
bond networks, F3/F4 order parameters, and TRACE cage perception + occupancy.
Scigantic MCP
MCP server for the Scigantic catalog of public scientific data archives. Search thousands of datasets and get LLM-ready schema cards without downloading anything.
Uniprot Link
MCP server for UniProt: protein function, sequence, features and cross-references over the UniProt SPARQL endpoint — intent-named tools plus a guarded raw-SPARQL escape hatch.
Spliceailookup Link
MCP server for SpliceAI Lookup (Broad Institute): SpliceAI, Pangolin and SpliceAI-10k splice-impact predictions for variants, plus an Ensembl VEP-backed variant resolver.
Encode Query Nexus
Best MCP Server for ENCODE Functional Genomics Data 2026 – Search, Download & Analyze Experiments
Clingen Link
MCP server for ClinGen (Clinical Genome Resource): gene–disease validity, dosage sensitivity, clinical actionability, and expert-panel variant pathogenicity (ERepo) — as typed too…
Gencc Link
MCP server for GenCC (Gene Curation Coalition): harmonized gene–disease validity classifications across member submitters, with consensus and conflict detection per gene–disease p…
Scikit
A unified life science data layer for your AI agents - genomics, proteomics, drug discovery, clinical trials across 300+ databases.
Reactome MCP
MCP server for the Reactome pathway database — search, lookup, hierarchy traversal, SBML/SBGN export, and gene-set pathway-enrichment analysis for any MCP-capable coding agent.
Eijex MCP
Public MCP access to Eijex bioinformatics, literature lookup, and FactorForge CDS review tools.
Hic MCP
MCP server for Hi-C / 3D-chromatin analysis: the open2c stack (cooler, cooltools) as agent tools over local .mcool files, with a real Micro-C dataset bundled so it runs offline.
Pd Target Identification
AI-powered multi-omics pipeline for Parkinson's Disease therapeutic target discovery and validation
Researcher Skill
Build focused research for Claude Code with one skill, three reference packs, and a clear workflow for mapping, judging, and synthesizing sources
Clinical Research MCP
MCP server for clinical research — PubMed papers, clinical trials, medical concepts. No API key needed.
Legumista
Legumista is an MCP server for Legume Information System projects
Highfold3 MCP
HighFold3 MCP server for peptide structure prediction
Cyclicchamp MCP
CyclicCHAMP MCP server for cyclic peptide modeling
Rag Pipeline Grounded LLM Genomics
LLM · RAG · MCP: a retrieval-augmented pipeline that answers questions over my ageing & exercise genomics research from papers and gene-level results, with cited, grounded answers…
Afcycdesign MCP
AF-CycDesign MCP server for cyclic peptide design with AlphaFold
Pepflow MCP
PepFlow MCP server for peptide structure generation
Metadome Link
MCP server for MetaDome: per-position missense tolerance (dN/dS) landscapes for human transcripts, Pfam domains, meta-domain homolog aggregation, and gnomAD/ClinVar per-position c…
Reprolith
Auto-reproduction & certification engine for the computational biomedical modeling literature — rebuild the model, re-run it, certify whether it reproduces its own results.
Pharmpapp MCP
PharmPApp MCP server for pharmaceutical peptide property prediction