get_pharmacophore_features
Pharmacophore mapping
How to use it
get_pharmacophore_features is exposed by the PubChem MCP Server MCP server. Add the server to your MCP client (Claude Desktop, Cursor, Windsurf and others), and the get_pharmacophore_features tool becomes available to the model automatically. See the full listing for setup details and every tool this server provides.
FULL PUBCHEM MCP SERVER LISTINGOther tools in PubChem MCP Server (29)
Synthetic accessibility
Chirality and isomer analysis
Lipinski Rule of Five analysis
Biodegradation analysis
Bulk processing (up to 200 compounds)
Comprehensive molecular descriptors
Cross-compound comparisons
3D structural information
Detailed assay protocols
All activity data for compounds
Detailed compound information by CID
Molecular weight, logP, TPSA, etc.
All names and synonyms
Links to ChEMBL, DrugBank, etc.
PubMed citations
FDA, EPA regulations
GHS hazard classifications
LD50, carcinogenicity data
ADMET predictions
Find biological assays
CAS Registry Number lookup
InChI/InChI key search
Exact SMILES string matching
Find compounds tested against targets
Search by name, CAS number, formula, or identifier
Chemical patent information
Tanimoto similarity search
Find compounds containing substructures
Find larger compounds containing query