Mychem vs Pubchem MCP Server
A side-by-side look at the Mychem and Pubchem 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 Mychem for biology & bioinformatics work as a local process; choose Pubchem MCP Server 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 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.
Choose Pubchem MCP Server when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- You prefer a local stdio subprocess transport.
- You want tools like
pubchem_search_compounds, pubchem_get_compound_details, pubchem_get_compound_image.
Feature & specification comparison
Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology & Bioinformatics | Biology & Bioinformatics |
| Quality signal | 45/100 · Fair | 55/100 · 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 | 10 |
| Directory activity | 1 views 0 installs 0 upvotes | 1 views 0 installs 0 upvotes |
| Tools | 3 | 10 |
| Full listing | View Mychem | View Pubchem MCP Server |
Tools & capabilities
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.
Pubchem MCP Server tools 10
pubchem_search_compoundsSearch for compounds by name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity, or list the compounds a bioassay found active.pubchem_get_compound_detailsGet physicochemical properties, descriptions, synonyms, drug-likeness, and classification for compounds by CID.pubchem_get_compound_imageFetch a 2D structure diagram (PNG) for a compound by CID.pubchem_get_compound_3d_structureFetch a 3D conformer (atomic coordinates and bonds) for a compound by CID, as parsed JSON or raw SDF.pubchem_get_compound_xrefsGet external database cross-references (PubMed, patents, genes, proteins, etc.).pubchem_get_compound_safetyGet GHS hazard classification and safety data for one or more compounds by CID (batch).pubchem_get_bioactivityGet a compound's bioactivity profile: assay results, targets, and activity values; filter by outcome or molecular target.pubchem_get_compound_interactionsGet drug-drug, drug-food, and chemical-target interactions for a compound by CID.pubchem_search_assaysFind bioassays by biological target (gene symbol, protein, Gene ID, UniProt accession).pubchem_get_summaryGet summaries for PubChem entities: assays, genes, proteins, taxonomy.
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.
Mychem
{
"mcpServers": {
"mychem": {
"command": "npx",
"args": [
"-y",
"@pipeworx/mcp-mychem"
]
}
}
}
Pubchem MCP Server
{
"mcpServers": {
"pubchem-mcp-server": {
"command": "bunx",
"args": [
"@cyanheads/pubchem-mcp-server@latest"
]
}
}
}
Frequently asked questions
Mychem is categorized under Biology & Bioinformatics and uses a local stdio subprocess. Pubchem MCP Server belongs to Biology & Bioinformatics and uses a local stdio subprocess. Pick Mychem for biology & bioinformatics work and Pubchem MCP Server 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.
Mychem has no declared pricing — check the project's own site. Pubchem MCP Server 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 mychem and pubchem-mcp-server as separate keys in the same mcpServers object, and your assistant will call tools from either one.
On AllMCPs, Mychem has a quality signal of 45/100 (Fair) with 1 views, 0 installs and 0 GitHub stars. Pubchem MCP Server has 55/100 (Good) with 1 views, 0 installs and 10 GitHub stars.