PubChem is one of the largest sources of publicly available chemical information, with more than 242.3 million depositor-provided substance descriptions, 94.7 million unique chemical structures, and 234.8 million bioactivity outcomes from 1.25 million assays covering around ten thousand unique protein target sequences.  This presentation provides an overview of PubChem’s data, tools, and services useful for drug discovery based on natural products.<br/><br/>        PubChem contains a large amount of bioactivity data, most of which are generated from high-throughput screening (HTS).  However, these data also include a substantial amount of bioactivity information extracted from scientific articles published in journals in the chemical biology, medicinal chemistry, and natural product domains, thanks to data contribution by other databases like ChEMBL, Guide to Pharmacology, BindingDB, and PDBbind.  In addition, through data integration with other databases such as DrugBank, HSDB, and HMDB, PubChem contains a wide range of annotations useful for drug discovery, including pharmacology, toxicology, drug target, metabolism, chemical vendors, scientific articles, patents, and many others.<br/><br/>        PubChem supports various types of chemical structure searches, including identify search, 2-D and 3-D similarity searches, substructure and superstructure searches, molecular formula search.  It also provides multiple programmatic access routes, including E-Utilities, Power User Gateway (PUG), PUG-SOAP, PUG-REST, and PUG-View, allowing one to build an automated workflow that takes advantage of information contained in PubChem.  In addition, through PubChemRDF, users can integrate PubChem’s data into their own in-house data on a local computing machine.

Exploiting PubChem for drug discovery based on natural products

256th National Meeting (2018)

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