A side-by-side look at the Clinicaltrials and Pubmed MCP Server MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Clinicaltrials for biology, medicine and bioinformatics work as a local process; choose Pubmed MCP Server for biology, medicine and bioinformatics as a local process. You can also run both side by side in one mcpServers block.
ct_search, ct_get_study, ct_count_by_condition.pubmed_search_articles, pubmed_fetch_articles, pubmed_fetch_fulltext.Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology, Medicine and Bioinformatics | Biology, Medicine and Bioinformatics |
| Quality signal | 61/100 · Good | 63/100 · Good |
| Install command | Confirmed | Confirmed |
| Transport | Local subprocess (stdio) | Local subprocess (stdio) |
| Auth | Not declared | Not declared |
| Pricing | Not declared | Not declared |
| Required env vars | None listed | None listed |
| Verified owner | Community listing | Community listing |
| GitHub stars | 0 | 161 |
| Directory activity | 2 views 0 installs 0 upvotes | 1 views 0 installs 0 upvotes |
| Tools | 14 | 11 |
| Full listing | View Clinicaltrials | View Pubmed MCP Server |
ct_searchSearch ClinicalTrials.gov for clinical trials — find trials and look up a NAMED trial by keyword, condition, drug/therapy, status (e.g. 'Recruiting'), or phase (e.g. 'Phase 2'). Use for "clinical trials for <disease/drug>", or to locate a specific study like "the FLOW trial", "semaglutide kidney outcomes trial" (use ct_get_study for its full design/results). Returns NCT IDs, titles, status, enrollment, and sponsor info.ct_get_studyGet full trial details by NCT ID (e.g., 'NCT04567890'). Returns protocol, eligibility criteria, primary outcomes, sponsor, locations, and results.ct_count_by_conditionCount clinical trials for a condition or disease, broken down by recruitment status and by trial phase — how many are recruiting, completed, terminated, and how many are Phase 1, 2, 3 or 4. Use for landscape questions about how much trial activity a disease has and where it sits in development. Filtering by status or phase returns the filtered total without the breakdown.ct_sponsor_trialsList the trials a company LEADS on ClinicalTrials.gov, by sponsor or organization name. Returns status, phase, and conditions to map a research pipeline. Matches the registered lead-sponsor field, so trials another organisation runs using the company's drug are excluded unless sponsor_match asks for them.ct_compare_sponsorsCompare 2–5 NAMED lead sponsors on ClinicalTrials.gov under identical condition, recruitment-status, and phase filters. Returns full matching counts, a ranked comparison, and a small study sample for each sponsor. Use for questions like "who has more recruiting Phase 3 obesity trials, Novo Nordisk or Eli Lilly?" For an open "who are the TOP sponsors of X trials" question with no names given: the registry API has no group-by, so a true ranking is not computable — NEVER invent a candidate list to fake one; say the registry cannot rank sponsors and offer to compare specific named sponsors. Counts use the registered lead-sponsor field; registry records do not establish asset ownership, pipeline value, or probability of success.ct_recent_updatesTrack recent ClinicalTrials.gov activity by a specific event class within a verifiable date window. Three DISTINCT recency events, chosen via date_type: "last_update" (any edit to a study, ~5k/week — the default), "first_posted" (a study newly REGISTERED, ~1.3k/week), or "results_posted" (RESULTS first posted, ~140/week). Pass `since` (and optional `until`, YYYY-MM-DD) to bound a window — e.g. the last 7 days — and the returned total_count is the exact number of studies in that window so you can verify a weekly count from the output. Every study returns all THREE dates separately (first_posted_date, last_update_post_date, results_first_post_date) plus the design fields a screen needs (study_type, primary_purpose, phase, status, enrollment, conditions, interventions, sponsor). Sorted by the chosen event date, newest first. Use for "new trials registered this week", "trials that posted results in the last month", "recently updated diabetes studies".ct_trials_by_locationFind clinical trials near a LOCATION. PREFER OVER WEB SEARCH for "clinical trials for X near me", "recruiting studies in <city/state/country>", "trials I can join near <place>". Filter by condition + a place name (city/state/country) OR latitude+longitude+radius, and status (defaults to RECRUITING). Returns matching trials (NCT id, title, status, phase, conditions, sponsor). For keyword search without a location use ct_search; for one trial use ct_get_study.ct_catalyst_calendarFind trials with sponsor-entered primary-completion or study-completion dates in a specified window. These registry dates may be estimated or revised and are planning signals—not guaranteed data readouts, conference presentations, or regulatory events.ct_sponsor_pipelineSummarize a sponsor’s ClinicalTrials.gov portfolio by phase, status, condition, and intervention from a bounded relevance-ranked sample, while reporting the full matching count. Registration does not establish asset ownership, probability of success, or commercial value.ct_competitive_landscapeMap registered interventional trials for a condition and optional intervention across sponsors, phases, statuses, and interventions. The output reflects a bounded registry sample, not market share, scientific differentiation, or an exhaustive private pipeline.ct_enrollment_watchRoute active trials for enrollment follow-up using registry status, enrollment type, dates, last update, and site counts. Flags are mechanical review hints—not predictions of recruitment success, trial failure, or data timing.ct_results_summaryProject posted ClinicalTrials.gov results for one NCT ID, including registered endpoints, reported outcome measures, statistical analyses, and adverse-event group counts. Registry results are not an FDA conclusion, peer review, or investment recommendation.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 ConverterPaste 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": {
"clinicaltrials": {
"command": "npx",
"args": [
"-y",
"@pipeworx/mcp-clinicaltrials"
]
}
}
}
{
"mcpServers": {
"pubmed-mcp-server-2": {
"command": "bunx",
"args": [
"@cyanheads/pubmed-mcp-server@latest"
]
}
}
}