PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public chemical database that collects chemical information from more than 500 data sources and disseminates it to the public free of charge. It contains the largest corpus of publicly available chemical data, with more than 235.7 million substance descriptions, 94.4 million unique chemical structures, and 232 million bioactivity outcomes from 1.2 million biological assay experiments, covering over 10 thousand protein targets.<br/><br/>PubChem provides various tools and services that exploit three-dimensional (3-D) molecular similarity in order to assist in the analysis of biologically similar molecules that are difficult to interrelate using traditional two-dimensional (2-D) similarity methods. The 3-D similarity search tool allows one to search PubChem for molecules similar to a query compound in terms of 3-D similarity. The 3-D structure clustering tool groups a set of compounds into clusters of 3-D similar compounds. The 3-D neighboring precomputes multi-conformer 3-D similarity search for each chemical and provides immediate access to a set of structurally similar compounds in PubChem as well as their respective superposition. The Structure-Activity Relationship (SAR) Analysis tool and the SAR Cluster database also support 3-D similarity, helping one to discover useful bioactivity data patterns.<br/><br/>This presentation will describe PubChem’s 3-D conformer models used for all the 3-D similarity-based tools and services in PubChem. For more than 90% of compounds, PubChem generates 3-D conformer models containing up to 500 conformers per compound. The PubChem conformer generation and sampling procedures are designed to ensure that 90% of the conformer models have at least one “bioactive” conformer whose (non-hydrogen atom pair-wise) RMSD from the experimentally determined conformation was closer than the upper-limit value predicted using an empirically derived equation. While most of the PubChem tools and services support up to 10 diverse conformers per compound, all conformers are accessible to the public.

How does PubChem generate computational 3-D structures of its compounds?

254th National Meeting (2017)

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