Similar compounds versus similar conformers: complementarity between PubChem 2-D and 3-D neighboring sets

Table 1 Number of compounds (CIDs) in the data sets employed in the present study

	Associated filters^a	Series A	Series B	Ratio (B/A) (%)
PubChem	all	36,017,715	31,776,025	88.2
MeSH	pccompound_mesh	82,446	62,217	75.5
Protein3D	pccompound_structure	22,753	17,387	76.4
PharmAct	pccompound_mesh_pharm	11,415	6977	61.1
Drug	pccompound_drugs	1773	950	53.6

The five data sets in Series A were generated using associated Entrez filters, which are used to restrict a search to a particular compound subset in PubChem. The five data sets in Series B were generated from their Series A counterparts by adding the parent compounds of the chemicals in the Series A data sets and then selecting those with a computed 3-D conformer description available
^aPubChem Compound Entrez filters allow users to retrieve CIDs that have a particular annotation type. For example, CIDs with “Drug” annotation can be retrieved via the URL: https://www.ncbi.nlm.nih.gov/pccompound/?term=pccompound_drugs[filter]

ISSN: 1758-2946