Clinicaltrialsgov MCP Server vs Mychem
A side-by-side look at the Clinicaltrialsgov MCP Server and Mychem MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Clinicaltrialsgov MCP Server for biology & bioinformatics work as a local process; choose Mychem for biology & bioinformatics as a local process. You can also run both side by side in one mcpServers block.
Which MCP server should you choose?
Choose Clinicaltrialsgov MCP Server when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- You prefer a local stdio subprocess transport.
- Its auth model fits you: No auth required.
- You want tools like
clinicaltrials_search_studies, clinicaltrials_get_study_record, clinicaltrials_get_study_count.
Choose Mychem when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- You prefer a local stdio subprocess transport.
- You want tools like
query, chem, metadata.
Feature & specification comparison
Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology & Bioinformatics | Biology & Bioinformatics |
| Quality signal | 63/100 · Good | 45/100 · Fair |
| Install command | Confirmed | Confirmed |
| Transport | Local subprocess (stdio) | Local subprocess (stdio) |
| Auth | No auth required | Not declared |
| Pricing | Free | Not declared |
| Required env vars | None listed | None listed |
| Verified owner | Community listing | Community listing |
| GitHub stars | 99 | 0 |
| Directory activity | 2 views 0 installs 0 upvotes | 1 views 0 installs 0 upvotes |
| Tools | 7 | 3 |
| Full listing | View Clinicaltrialsgov MCP Server | View Mychem |
Tools & capabilities
Clinicaltrialsgov MCP Server tools 7
clinicaltrials_search_studiesSearch studies with full-text and field-specific queries, status/phase/geographic filters, pagination, sorting, and field selectionclinicaltrials_get_study_recordFetch a single study by NCT ID — full protocol record with optional location/outcome/reference capsclinicaltrials_get_study_countFast total study count for a query, without fetching dataclinicaltrials_get_field_valuesDiscover valid values for API fields, with per-value study countsclinicaltrials_get_field_definitionsResolve valid field names — keyword search, path drill-down, or top-level overviewclinicaltrials_get_study_resultsFetch posted results — outcomes, adverse events, participant flow, baseline — for completed studiesclinicaltrials_find_eligibleMatch patient demographics and conditions to candidate recruiting trials, without checking inclusion/exclusion criteria
Mychem tools 3
querySearch MyChem.info for drugs / chemical compounds. Accepts a plain drug name ("aspirin"), an InChIKey, or a fielded query (e.g. "chembl.pref_name:aspirin", "drugbank.name:Acetylsalicylic acid"). Returns aggregated hits with cross-references to ChEMBL, DrugBank, PubChem, ChEBI, DrugCentral, etc. Use…chemFetch the full aggregated annotation for a single chemical / drug by id. The id is typically an InChIKey (e.g. "BSYNRYMUTXBXSQ-UHFFFAOYSA-N"), but a DrugBank id, ChEMBL id, or other source id also works. Returns merged annotations from ChEMBL, DrugBank, PubChem, ChEBI, DrugCentral, etc., including…metadataReturns MyChem.info build metadata: total indexed compound count, available annotation sources (ChEMBL, DrugBank, PubChem, ChEBI, DrugCentral, FDA NDC), and their current release versions.
Ready-to-paste client configs
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.
Clinicaltrialsgov MCP Server
{
"mcpServers": {
"clinicaltrialsgov-mcp-server": {
"command": "npx",
"args": [
"-y",
"clinicaltrialsgov-mcp-server"
]
}
}
}
Mychem
{
"mcpServers": {
"mychem": {
"command": "npx",
"args": [
"-y",
"@pipeworx/mcp-mychem"
]
}
}
}
Frequently asked questions
Clinicaltrialsgov MCP Server is categorized under Biology & Bioinformatics and uses a local stdio subprocess. Mychem belongs to Biology & Bioinformatics and uses a local stdio subprocess. Pick Clinicaltrialsgov MCP Server for biology & bioinformatics work and Mychem for biology & bioinformatics.
Copy the mcpServers block from the config section on this page into your client's config (for example claude_desktop_config.json or ~/.cursor/mcp.json), then fully restart the client.
Clinicaltrialsgov MCP Server is listed as free. Auth: no auth required. Mychem has no declared pricing — check the project's own site. If a server needs environment variables such as API keys, define them under the env key in your client's MCP config.
Yes. MCP clients support multiple servers: add clinicaltrialsgov-mcp-server and mychem as separate keys in the same mcpServers object, and your assistant will call tools from either one.
On AllMCPs, Clinicaltrialsgov MCP Server has a quality signal of 63/100 (Good) with 2 views, 0 installs and 99 GitHub stars. Mychem has 45/100 (Fair) with 1 views, 0 installs and 0 GitHub stars.