A comprehensive Model Context Protocol (MCP) server for accessing the PubChem chemical database. This server provides access to over 110 million
Unofficial PubChem MCP server exists for a simple reason — assistants are far more useful when they can act on Unofficial PubChem directly instead of describing what you should do. A comprehensive Model Context Protocol (MCP) server for accessing the PubChem chemical database. This server provides access to over 110 million chemical compounds with extensive molecular properties, bioassay data, and chemical.
Setup follows the usual MCP pattern — install or clone the server, register it in your client's configuration file, restart the client.
Once Unofficial PubChem is connected, these are the calls the assistant has available:
search_compounds — Search by name, CAS number, formula, or identifierget_compound_info — Detailed compound information by CIDsearch_by_smiles — Exact SMILES string matchingsearch_by_inchi — InChI/InChI key searchsearch_by_cas_number — CAS Registry Number lookupget_compound_synonyms — All names and synonymssearch_similar_compounds — Tanimoto similarity searchsubstructure_search — Find compounds containing substructuressuperstructure_search — Find larger compounds containing queryget_3d_conformers — 3D structural informationanalyze_stereochemistry — Chirality and isomer analysisget_compound_properties — Molecular weight, logP, TPSA, etcThis sits in the database access group, where several servers overlap in what they claim to do but differ sharply once you actually set them up. Unofficial PubChem's toolset — search_compounds, get_compound_info, search_by_smiles and 11 more — is a fair guide to whether it matches your workflow. It is maintained by Augmented-Nature; worth a glance at recent repository activity before you build anything load-bearing on it.
This entry was verified against Unofficial PubChem's own documentation before publication; SyncDev keeps the directory reviewed rather than auto-generated.
| 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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