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Table 3 Performance of 3-D neighboring.

From: PubChem3D: Similar conformers

  Diverse Conformer Count
  1 3 5 7 10
Total Conformer Pairs (billions) 110 866 2,200 4,010 7,510
CT Feature Filter 65.7% 65.2% 65.0% 64.9% 64.7%
CT Volume Filter 0.2% 0.2% 0.2% 0.2% 0.2%
ST Volume Filter 2.9% 2.7% 2.6% 2.5% 2.3%
Alignment Recycling Fingerprint 4.4% 4.5% 4.5% 4.6% 4.7%
Alignment Recycling Overlap 26.5% 27.2% 27.5% 27.7% 27.9%
Insufficient ST (billions) 0.2 1.3 2.9 5.0 8.5
Insufficient CT (billions) 0.1 0.6 1.4 2.1 3.4
Neighbor Count (millions) 1.8 6.1 10.7 15.5 22.3
Compound Pairs per second 155,871 18,632 7,829 4,301 2,261
Conformer Pairs per second 155,871 146,318 156,241 156,618 153,959
Total Search Time (days) 8.2 68.5 163.1 296.9 564.9
Filtering Time 0.9% 0.8% 0.8% 0.7% 0.7%
Alignment Recycling Time 82.6% 86.0% 86.8% 86.8% 86.7%
Superposition Optimization Time 10.4% 10.0% 9.9% 10.2% 10.7%
Other Overhead Time 6.1% 3.2% 2.5% 2.3% 1.9%
Input data size (GB) 19 50 83 114 159
  1. Performance of 3-D neighboring 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.