PubChem3D: Shape compatibility filtering using molecular shape quadrupoles

Table 4 Acceleration of PubChem 3-D neighboring using the quadrupole filter

	Diverse Conformer Count
	1	3	5	7	10
Average Query Conformers per compound	1.0	2.7	4.1	5.4	7.2
Average Search Conformers per compound	1.0	3.0	4.9	6.7	9.4
Total Compound Pairs (billions)	110	110	110	110	110
Total Conformer Pairs (billions)	110	866	2,200	4,010	7,510
Total Search Time before (days)	8.2	68.5	163.1	296.9	564.9
Total Search Time after (days)	6.5	55.3	118.5	224.4	410.9
Conformer pair throughput (thousands/sec)	196	181	215	207	212
% Speed up	26%	24%	38%	32%	38%

Change in throughput as a result of quadrupole filtering when generating 3-D neighbors as a function of diverse conformer count for the 4,218 chemical structures (Query) with known biological function when neighbored against the entire "live" PubChem3D contents (Search) of 26,157,365 small molecules.

ISSN: 1758-2946