How do I connect a Biology & Bioinformatics MCP server to Claude Desktop or Cursor?

To install a Biology & Bioinformatics MCP server, select your desired server from the directory, copy the JSON configuration snippet, and add it to your client config file (such as claude_desktop_config.json or .cursor/mcp.json).

Are Biology & Bioinformatics MCP servers free to use?

Yes, all Biology & Bioinformatics MCP servers listed in this directory are open-source and free to integrate into compatible Model Context Protocol clients.

98 Biology & Bioinformatics MCP Servers

Q: What are Biology & Bioinformatics Model Context Protocol (MCP) servers?

Model Context Protocol (MCP) servers in the Biology & Bioinformatics category allow AI assistants (such as Claude Desktop, Cursor, Windsurf, and Cline) to connect directly to biology & bioinformatics tools, APIs, and databases without manual copy-pasting.

Discover 98 Biology & Bioinformatics MCP servers for AI agents. Browse, compare, and install Model Context Protocol tools that connect Claude, Cursor, and other clients to biology & bioinformatics capabilities. Popular picks include HealthChain, Codeindex, Folklore Clinical Variant Interpretation MCP.

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HealthChain

healthchainai

Typed, validated FHIR tools for healthcare AI agents — build, read, validate, and code FHIR resources from a patient bundle, with terminology lookup and machine-readable validation reports built for fix-and-retry. pip install healthchain[mcp]

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Codeindex

Structural code intelligence over MCP: symbols, callers, imports and blast radius, 40+ languages.

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Folklore Clinical Variant Interpretation MCP

Folklore MCP 1.5.0 is Helena Bioinformatics’ public, read-only bioinformatics MCP for genomic variant interpretation, ClinGen gene-disease evidence and literature. Seven tools include get_gene_disease_associations (gene symbol/HGNC ID to diseases) and search_disease_genes (MONDO ID/disease name to genes), preserving inheritance, source classifications and provenance. Existing GRCh38 germline variant and literature tools remain available, alongside the optional support_helena helper. Streamable HTTP; no account or API key. No patient data, raw DNA/VCF ingestion or batch processing. Results require professional review and are not diagnoses.

Verified

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Molecare MCP

Educational dermatology knowledge and lesion tooling. No credentials needed. Not a medical device.

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Omophub MCP

Search, lookup, map, and navigate OMOP medical vocabularies via AI agents

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Noodle Biomedical Literature Discovery MCP

Official public, read-only Model Context Protocol server from Helena Bioinformatics for biomedical literature discovery. Agents can search PubMed and scholarly research, resolve PMID, DOI, and PMCID identifiers, inspect publication metadata, find related papers, traverse bounded citation graphs, explore semantic literature neighborhoods, and check corpus coverage. Use the hosted Streamable HTTP endpoint https://api.helena.bio/noodle/v1/mcp; no npm or npx package is required.

Verified

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Spiderbrain

Deterministic context layer for your codebase: change impact, blast radius, answers with receipts.

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Pubmed MCP Server

Comprehensive PubMed MCP Server to search, retrieve, and analyze biomedical literature from NCBI.

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Dingdawg Healthcare Agent

HIPAA-aware healthcare AI. Clinical documentation, compliance checks, audit prep. Free local tier.

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Phi Longevity Prism

Analyze biomarker panels with an MD-led clinical engine. Guideline-cited. Synthetic data only.

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Sourcebook

Live codebase intelligence for AI agents: conventions, blast radius, import graphs, git insights.

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Code Impact MCP

Dependency graph & blast-radius analysis for TypeScript/JS. Predict breaks before commit.

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Wcagc MCP

WCAG-Compliance

Deterministic axe-core accessibility scanning (WCAG 2.1 AA, EN 301 549, PDF/UA) through a wcagc account: scan any public URL or PDF, crawl a whole registered site, replay saved multi-step journeys, and read violation trends. Returns structured findings — rule, severity counts and the success criteria involved — so the assistant reasons over real results rather than guessing from markup. Every scan result carries an automated-coverage disclaimer instead of a score or a pass/fail verdict. Hosted at https://mcp.wcagc.com/mcp, or run it locally with npx -y @wcagc/mcp.

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Fhirfly MCP Server

Healthcare reference data: drugs, providers, diagnoses, labs, vaccines, and claims via 28 tools.

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Prism

Local-first repo intelligence for agents: DNA, health, blast radius, and Dispatch jobs.

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Supplement Advisor MCP

Evidence-based supplement guidance: clinical doses, form comparisons, interactions, cost-per-dose.

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Automatedrcm Billing MCP

Medical-billing tools for AI agents: prior-auth checks, denial decoding, claim triage, appeals.

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Galaxy MCP

MCP server for Galaxy bioinformatics platform - connect, execute tools, and manage workflows

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Dep Oracle

Predictive dependency security engine. Trust scores, zombie detection, blast radius analysis.

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Rosetta MCP Server

Rosetta/PyRosetta protein modeling and Biotite translation for computational biology

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Repo Graph

James-Chahwan

Structural graph map of any codebase for AI coding assistants. Scans entities, relationships, and feature flows across 13 languages so LLMs navigate by structure instead of grepping through everything.

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Sniff MCP

Canine genomics for agents: breed allele frequencies + AI pathogenicity over the open Sniff Atlas

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Pubchem MCP Server

MCP server for PubChem. Search compounds, properties, safety, bioactivity, xrefs, and summaries.

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Protein MCP Server

Federated protein structure & function across experimental (PDB) and predicted (AlphaFold) models.

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Medplum MCP

Securely access and manage FHIR healthcare data stored in Medplum.

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Causely

Causal reasoning for reliability: root cause, blast radius, and service health for agents.

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RCSB PDB

MCP server to search, inspect, and cross-reference RCSB Protein Data Bank structures

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MCP Code Indexer

Nishant-Chaudhary5338

Index any TypeScript/React repo (including monorepos) into a queryable code graph. Reverse queries (who-renders, who-calls, find-references), blast-radius analysis, dependency cycles, dead-code orphans, and symbol signatures — exposed over stdio. Install: npx code-graph-indexer.

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Appendix

Physician-reviewed medical opinions and prescriptions for AI agents.

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Medical Codes MCP Server

Offline US medical code lookup and crosswalk — ICD-10-CM, ICD-10-PCS, HCPCS Level II. Keyless.

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Uniprot MCP Server

Protein research over UniProtKB — search by function, fetch curated records, map IDs, proteomes.

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Puumed

PubMed MCP — wraps the NCBI E-utilities API (biomedical literature, free, no auth)

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Chembl MCP Server

Link compounds to protein targets, rank bioactivity, and look up drug mechanisms and indications.

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Npi Providers MCP Server

Look up US healthcare providers in the NPPES NPI registry and resolve NUCC specialty codes.

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GWAS Bioinformatics MCP Server

Access 30+ bioinformatics tools from 14 databases.

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MCP Blast Radius

aos-standard

MCP Blast-Radius Auditor — static blast radius extraction and AOS manifest.json divergence gate (Oracle / Permitted / Prohibited). Stdio MCP (mcp-blast-radius) plus CI blocking gate (mcp-blast-radius-gate). Install: pip install mcp-blast-radius==0.2.0 · PyPI

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OpenFDA Regulatory Metadata

Resolve FDA application numbers and product names to regulatory metadata (CDER, CBER, CDRH).

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Blast Scope

Contextual blast-radius scoring for shell commands an AI agent is about to run

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Vortex Iq

Read-only access to your VortexIQ store data: audits, KPIs, alerts, Brand DNA, reports, Ask VIQ.

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MCP Pharma

Drug reference: GRLS, VEDL prices, Roszdravnadzor series recalls. Not medical advice.

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API Governance

API governance for AI agents. Detects breaking changes, scores blast radius, blocks unsafe calls.

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Costkits MCP

MCP server for CostKits: live healthcare procedure cost estimates and provider pricing.

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Dieta.ai

Nutrition tracking by Dieta.ai. Read your food log with macros (calories, protein, carbs, fat, fiber

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Alphafold

AlphaFold DB MCP — predicted protein structures.

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Cbioportal

cBioPortal MCP — cancer genomics portal.

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Ensembl

Ensembl REST — vertebrate genomes, sequences, comparative genomics, variation

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Fda Devices

FDA medical-device regulatory intelligence from keyless openFDA datasets.

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Interpro

InterPro MCP (EBI) — protein family / domain / functional-site classification.

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Medical Codes

Medical codes MCP.

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Mesh

NLM MeSH (Medical Subject Headings) MCP.

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Mygene Info

MyGene.info — gene annotation joining NCBI/Ensembl/UniProt/KEGG/OMIM

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Ncbi Eutils

NCBI E-utilities — federated Entrez search/fetch (PubMed/Gene/Nucleotide/…)

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Pdbe

PDBe (Protein Data Bank in Europe, EBI) MCP.

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Protein Atlas

Human Protein Atlas (HPA) MCP — keyless.

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Rcsb Pdb

RCSB PDB MCP — experimentally determined macromolecular structures.

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String Db

STRING protein-protein interaction networks across ~12k organisms

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Vascue Public Knowledge Search

Search Vascue's public healthcare-ops, insurance-claims and booking docs. Public content only.

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Sense

Codebase understanding for AI coding agents — symbol graph, blast radius, semantic search.

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Service Public France

French public services: tax, property, admin, education, healthcare, security, risks, legal texts

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Hormonaly Clinical Intelligence

24 tools for evidence-graded clinical queries, hormones, peptides, longevity & drug interactions.

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Browse all 98 Biology & Bioinformatics servers →

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Frequently Asked Questions about Biology & Bioinformatics MCP Servers

Model Context Protocol (MCP) servers in the Biology & Bioinformatics category allow AI assistants (such as Claude Desktop, Cursor, Windsurf, and Cline) to connect directly to biology & bioinformatics tools, APIs, and databases without manual copy-pasting.