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

From: PubChem3D: Shape compatibility filtering using molecular shape quadrupoles

  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%
  1. 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.