Explore the community PubChem MCP project for compound searches, molecular properties and bioassay data. Check identifiers, source records and setup instructions.
This community PubChem MCP project connects an assistant to chemical database information. The maintainer describes compound search, molecular properties, structure and similarity queries, bioassay records and links to related databases.
Start with the compound name or identifier, then inspect the returned PubChem CID and structure. Similar names can refer to different records. Keep the identifier with the result when asking for additional properties or comparing compounds.
The source documents a search_compounds request and a workflow for retrieving detailed compound information. Check the tool names discovered by the connected client before using a more specialised operation; the README's feature groups are broader than a single universal request.
The maintainer's installation guide uses npm install, npm run build and npm start from the source project. Follow the repository for the current client connection details rather than substituting an unrelated package with a similar name.
Ask for units and the referenced record alongside a reported property. For bioassay or similarity results, retain the query criteria so the comparison can be repeated. Trace the returned information to the corresponding source record when it matters to the task.
Check the linked publisher documentation and your connected client's tool list. Names and availability can vary with the server version and account permissions.
| Tool | What it does |
|---|---|
| search_compounds | Search by name, CAS number, formula, or identifier |
| get_compound_info | Detailed compound information by CID |
| search_by_smiles | Exact SMILES string matching |
| search_by_inchi | InChI/InChI key search |
| search_by_cas_number | CAS Registry Number lookup |
| get_compound_synonyms | All names and synonyms |
| search_similar_compounds | Tanimoto similarity search |
| substructure_search | Find compounds containing substructures |
| superstructure_search | Find larger compounds containing query |
| get_3d_conformers | 3D structural information |
| analyze_stereochemistry | Chirality and isomer analysis |
| get_compound_properties | Molecular weight, logP, TPSA, etc. |
| calculate_descriptors | Comprehensive molecular descriptors |
| predict_admet_properties | ADMET predictions |
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