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.

97 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 97 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, Maccabi Health, MCP Airlock.

Open in interactive directory

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]

4 1 1

Maccabi Health

Read your own Maccabi Healthcare records: labs, prescriptions, visits, referrals, PDFs.

0 0 0

MCP Airlock

Governance proxy for MCP servers: allowlist, forced dry run, human confirmation, blast radius, audit

0 0 0

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

5 0 0

Codeindex

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

2 0 0

Prism

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

2 0 0

Omophub MCP

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

1 0 0

Molecare MCP

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

1 0 0

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

6 0 0

Alphafold

AlphaFold DB MCP — predicted protein structures.

0 0 0

Dingdawg Healthcare Agent

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

2 0 0

String Db

STRING protein-protein interaction networks across ~12k organisms

2 0 0

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.

2 0 0

Mhra Uk

MHRA (UK Medicines and Healthcare products Regulatory Agency) — the public

0 0 0

Pdbe

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

2 0 0

Rcsb Pdb

RCSB PDB MCP — experimentally determined macromolecular structures.

0 0 0

Ncbi Eutils

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

1 0 0

Interpro

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

0 0 0

OpenFDA Regulatory Metadata

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

1 0 0

Ensembl

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

0 0 0

Mesh

NLM MeSH (Medical Subject Headings) MCP.

0 0 0

Protein Atlas

Human Protein Atlas (HPA) MCP — keyless.

0 0 0

Cbioportal

cBioPortal MCP — cancer genomics portal.

0 0 0

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.

2 0 0

Ncbi Variation

dbSNP refSNP records and HGVS/SPDI/rsID normalization for human genetic variants, from NCBI…

0 0 0

Ncbi Datasets

NCBI Datasets — the US National Library of Medicine's genome, gene and taxonomy reference service…

0 0 0

Bold Systems

BOLD Systems (Barcode of Life Data System, University of Guelph) — the global DNA barcode…

0 0 0

Bindingdb

BindingDB — measured protein/small-molecule binding affinities.

0 0 0

Costkits MCP

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

0 0 0

Galaxy MCP

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

0 0 0

Dep Oracle

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

1 0 0

Automatedrcm Billing MCP

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

1 0 0

Rosetta MCP Server

Rosetta/PyRosetta protein modeling and Biotite translation for computational biology

3 0 0

Candor

Per-function effect analysis for agents: blast radius, what reaches the network, gate verdicts.

0 0 0

Healthcare AI Governance MCP

Healthcare Ai Governance automation via MCP. Includes classify samd, check cds exemption, hi...

1 0 0

Pubchem MCP Server

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

0 0 0

Hipaa Compliance MCP

HIPAA healthcare compliance assessment tools for AI agents. Capabilities: assess safeguards,...

0 0 0

Protein MCP Server

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

1 0 0

Service Public France

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

0 0 0

Healthcare Fhir MCP

Healthcare Fhir tools for AI agents. Capabilities: search patients, get patient, search cond...

1 0 0

RCSB PDB

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

0 0 0

Causely

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

0 0 0

Sourcebook

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

0 0 0

Appendix

Physician-reviewed medical opinions and prescriptions for AI agents.

2 0 0

Uniprot MCP Server

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

1 0 0

Gramps MCP MCP Server

MCP server for Gramps genealogy via the Gramps Web API: CRUD, search, merge, timelines, DNA.

0 0 0

Npi Providers MCP Server

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

1 0 0

Puumed

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

1 0 0

Loa Healthcare Pricing

Search source-labeled hospital prices, CPT codes, providers, and healthcare cost estimates.

0 0 0

GWAS Bioinformatics MCP Server

Access 30+ bioinformatics tools from 14 databases.

0 0 0

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

2 0 0

Vortex Iq

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

1 0 0

Blast Scope

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

1 0 0

Fhirfly MCP Server

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

0 0 0

Mdr Medical Device MCP

EU MDR (Reg 2017/745) and IVDR (Reg 2017/746) compliance for medical device + IVD manufacturers...

0 0 0

MCP Pharma

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

0 0 0

ClinicMarketIQ Public Data

Read-only U.S. healthcare dataset metadata, schemas, immutable downloads, and checksums.

0 0 0

Dieta.ai

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

0 0 0

Mygene Info

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

0 0 0

Opentreeoflife

Open Tree of Life MCP.

0 0 0

Browse all 97 Biology & Bioinformatics servers →

Explore related categories

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.