Topic · updated 2026-10-05
Biomedical & PubMed MCP servers
50 Biomedical & PubMed MCP servers indexed on awesomemcp.in. Every entry links to a live GitHub repository with a known author, is de-duplicated across the official MCP registry and community lists, and carries an automated vulnerability-check badge. Built by @andybrandt, @cyanheads, @musharna, @rewire-bio, @Hormonaly-ai and 35 other authors.
Top 50 Biomedical & PubMed MCP servers
Search and read medical and life sciences papers from PubMed.
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★ 172
2026-03-19Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms.
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★ 153
2026-10-04Plant genomics MCP — 56 tools across 23 backends with cross-source synthesis.
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★ 7
2026-10-01Bounded genomic data from archives and indexed files, with versioned reference evidence.
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★ 3
2026-10-0224 tools for evidence-graded clinical queries, hormones, peptides, longevity & drug interactions.
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★ 2
2026-10-03Search PubMed and summarize biomedical literature.
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★ 2
2026-05-30Bioinformatics MCP for genomic variant interpretation, gene-disease evidence and literature.
Risk found
★ 1
2026-09-11PubMed MCP — wraps the NCBI E-utilities API (biomedical literature, free, no auth)
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★ 1
2026-09-30Search biomedical papers, inspect publication records, and traverse citation or semantic graphs.
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★ 0
2026-09-01MCP server for Firecrawl — web search, scraping, and biomedical/arXiv paper search.
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★ 7,554
2026-10-05Access biomedical research data from PubMed, ClinicalTrials.gov and MyVariant.info.
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★ 646
2026-10-05Query medical information, drug databases, drug interactions and clinical guidelines.
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★ 113
2026-10-01Search ClinicalTrials.gov — find studies, retrieve results, match patients to eligible trials.
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★ 97
2026-10-05Schema-enforced spatial transcriptomics analysis with 20 tools and 66 methods via MCP
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★ 45
2026-09-29Unofficial MCP server connecting OpenEvidence to AI agents via authenticated browser sessions
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★ 43
2026-09-25Map clinical terminology to OMOP concepts using LLMs for healthcare data standardization and interoperability.
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★ 41
2026-05-11MCP server for Galaxy bioinformatics platform - connect, execute tools, and manage workflows
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★ 39
2026-10-04Query the BioThings API for genes, genetic variants, drugs and taxonomic information.
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★ 35
2025-11-03Bioinformatics toolkit for genomics queries and analysis, wrapping the gget library.
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★ 32
2025-10-2720 MCP tools + 48 skills for ENCODE Project genomics — search, download, pipelines
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★ 21
2026-09-27Open Targets MCP server for targets, diseases, drugs, variants, and evidence
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★ 19
2026-09-21MCP server that receives results from clinical/lab analyzers over ASTM E1381/E1394 (CLSI LIS1/LIS2).
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★ 17
2026-09-26PubMed & Europe PMC literature search, US/UK drug labelling, and clinical trials for AI assistants.
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★ 15
2026-09-29NCBI and PubMed literature search with analytics, caching, MeSH integration, related article discovery and batch processing for life sciences research.
Needs review
★ 13
2025-06-28Checks every LaTeX reference against Crossref, dblp, arXiv, DataCite, PubMed and OpenAlex. No LLM.
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★ 12
2026-10-05Biomedical MCP server: genes, variants, trials, literature, patents, optional SQL/R/biowasm tools.
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★ 12
2026-10-05Search PubChem compounds, properties, safety data, bioactivity, and cross-references.
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★ 9
2026-09-25Search and analyse scientific literature across Europe PMC, PubMed, arXiv, and ClinicalTrials.gov
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★ 8
2026-10-05Search, lookup, map, and navigate OMOP medical vocabularies via AI agents
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★ 6
2026-09-07MCP gateway federating 22 biomedical MCP servers behind one endpoint: gnomAD, ClinVar, HPO, VEP.
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★ 6
2026-10-04MCP Server for 3D protein structural data retrieval & analysis from RCSB PDB, PDBe, and UniProt.
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★ 6
2026-09-22Search open-source research papers across arXiv, OpenAlex, Crossref, PubMed, Semantic Scholar.
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★ 6
2026-10-03Interact with the UCSC Genome Browser API to find genomes, chromosomes and more.
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★ 6
2025-11-13Academic, code and medical-regulatory trend monitoring across arXiv, PubMed, GitHub, Hugging Face and openFDA, with newspaper-style briefings.
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★ 6
2026-10-05Forensic biopharma catalyst auditor — 10 tools, deterministic CLEAN/BEAR_SIGNAL verdict.
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★ 5
2026-05-11Search and retrieve bioRxiv and medRxiv preprints — by DOI, date interval, or keyword — via MCP.
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★ 4
2026-09-23Collaborative BrAPI v2.1 MCP workspace — studies, germplasm, genotypes across Breedbase, T3, more.
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★ 4
2026-10-04Find & fetch research datasets across 17 archives, omics registries, and literature sources.
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★ 4
2026-10-05MCP server for AlphaFold and 8 other biomedical data sources with a local SQLite knowledge graph
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★ 4
2026-10-05Look up genes, sequences, variants, homologs, and cross-database xrefs from Ensembl REST.
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★ 3
2026-09-24Search 35M+ PubMed, 400K+ ClinicalTrials.gov & ISRCTN trials. Prompts included. No API key.
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★ 3
2026-07-13Verifiable, release-aware protein evidence workflows over UniProt and linked scientific sources.
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★ 3
2026-10-05Run reproducible Nextflow bioinformatics pipelines with verifiable Workflow Run RO-Crate provenance: container digests, tool versions and checksums.
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★ 2
2026-08-18Search 340M+ academic papers — citation graphs, semantic similarity, and AI literature reviews.
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★ 1
2026-06-08HIPAA-aware healthcare AI. Clinical documentation, compliance checks, audit prep. Free local tier.
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★ 1
2026-08-06Search arXiv/Semantic Scholar/OpenAlex + medical evidence (PubMed/Europe PMC) + LaTeX/PDF tools.
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★ 1
2026-07-24Linked life-science search: 43M+ papers, 1.2M+ trials, drugs, genes, FDA/EMA approvals, patents.
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★ 1
2026-09-29Headless PyMOL for molecular visualization, GROMACS/LAMMPS trajectories and clathrate-hydrate cage analysis, including H-bond networks and order parameters.
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★ 1
2026-09-02Bio-robotics engine that converts biological data from the UniProt API into Cartesian G-code coordinates.
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★ 0
2026-10-02Clinical audit of Glooko diabetes data from any pump or CGM: time in range, GMI, trends and bolus/basal analysis, adapting to the data your devices report.
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★ 0
2026-09-15
Quick install
Add the most popular option to Claude Code:
claude mcp add mcp-simple-pubmed -- uvx mcp-simple-pubmed
FAQ
What is the best biomedical & pubmed mcp server?
By GitHub stars, the most popular is mcp-simple-pubmed by @andybrandt (172 stars). awesomemcp.in lists 50 MCP servers for this topic, ranked by official status and popularity.
Are these MCP servers safe to install?
47 of 50 passed our automated vulnerability check (OSV.dev advisories for the published package, OpenSSF Scorecard, license, maintenance and provenance). The check is automated and does not guarantee 100% safety — review the code and permissions before installing.
How do I install mcp-simple-pubmed?
With Claude Code: claude mcp add mcp-simple-pubmed -- uvx mcp-simple-pubmed. Every listing on awesomemcp.in includes an install command and, where available, an mcp.json snippet for Claude Desktop, Cursor and other MCP clients.
Can AI agents read this list?
Yes. The full catalog is available as JSON at https://awesomemcp.in/api/mcps.json and https://awesomemcp.in/api/skills.json, and as plain text at https://awesomemcp.in/llms.txt.