A side-by-side look at the Pubmed MCP Server and Decoder 3am MCP MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Pubmed MCP Server for biology, medicine and bioinformatics work as a local process; choose Decoder 3am MCP for biology, medicine and bioinformatics over a hosted endpoint. You can also run both side by side in one mcpServers block.
pubmed_search_articles, pubmed_fetch_articles, pubmed_fetch_fulltext.classify_sleep_cause, get_cause_info, list_causes.Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology, Medicine and Bioinformatics | Biology, Medicine and Bioinformatics |
| Quality signal | 63/100 · Good | 52/100 · Good |
| Install command | Confirmed | Confirmed |
| Transport | Local subprocess (stdio) | Remote HTTP/SSE |
| Auth | Not declared | No auth required |
| Pricing | Not declared | Free |
| Required env vars | None listed | None listed |
| Verified owner | Community listing | Community listing |
| GitHub stars | 161 | 1 |
| Directory activity | 1 views 0 installs 0 upvotes | 3 views 0 installs 0 upvotes |
| Tools | 11 | 4 |
| Full listing | View Pubmed MCP Server | View Decoder 3am MCP |
pubmed_search_articlesSearch PubMed with full query syntax, structured filters, date ranges, and optional summariespubmed_fetch_articlesFetch article metadata by PMID: abstract, authors, journal, MeSH terms, grants, a collective author's investigators on request, linked retraction and correction noticespubmed_fetch_fulltextFetch full text by PMID, PMCID, or DOI, falling back from PMC to Europe PMC to Unpaywallpubmed_europepmc_searchSearch Europe PMC for preprints, patents, Agricola, and open-access records PubMed doesn't carrypubmed_europepmc_fetchFetch complete Europe PMC records, including the untruncated abstract, as `records: [{ source, epmcId }]pubmed_format_citationsFormat citations in APA 7th, MLA 9th, BibTeX, RIS, or Vancouver (ICMJE/NLM), with linked retraction and correction noticespubmed_find_relatedFind similar articles, citing articles, or references for a PMIDpubmed_spell_checkCorrect a misspelled PubMed query via NCBI ESpellpubmed_lookup_meshLook up MeSH headings with tree numbers, scope notes, and entry termspubmed_lookup_citationResolve partial references, up to 25 at a time, to PMIDs via ECitMatchpubmed_convert_idsConvert between DOI, PMID, and PMCID via the PMC ID Converterclassify_sleep_causeClassify the likely primary cause of sleep disruption from a symptom description.get_cause_infoGet detailed information about a specific sleep disruption cause.list_causesList all 5 sleep disruption causes with summaries.get_decoder_urlGet a tracked URL to the full interactive 3AM Decoder.Paste either block (or both) into your client config, e.g. claude_desktop_config.json or ~/.cursor/mcp.json. We only show a config when the install command is confirmed.
{
"mcpServers": {
"pubmed-mcp-server-2": {
"command": "bunx",
"args": [
"@cyanheads/pubmed-mcp-server@latest"
]
}
}
}
{
"mcpServers": {
"thelongevityvault-decoder-3am-mcp": {
"url": "https://decoder-3am--thelongevityvault.run.tools/sse"
}
}
}