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Table 2 Compounds generated by RetroPath2.0 using various reaction rules applied on E. coli iJO1366 model metabolites [43]

From: Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0

Reaction rule set No. of compounds generated E. coli model coverage (1) MS peaks coverage (2) Median no. of compounds per peak Averaged no. of compounds per peak
E. coli model [43] 751 100.0 12.3 1 1.5
Sympheny [9] 9448 48.2 40.4 3 6.3
BNICE [42] 8421 68.8 45.3 3 5.8
D16 (3) 1230 82.0 23.1 1 2.0
D10 2992 83.6 25.6 1 2.3
D8 5055 84.2 28.1 1 2.7
D6 11,981 84.7 46.6 2 3.1
D4 37,450 86.8 60.6 2 5.7
D2 162,480 91.7 79.9 8 16.9
  1. All numbers correspond to compounds having different InChIs at the connectivity level
  2. (1) The E. coli model contains 751 compounds (with different connectivity InChIs). The column reports the % of these 751 compounds generated by the different rule sets. (2) The MS spectra were downloaded from Metabolight [44] and the OpenMS workflow described in the “Methods” section retrieved a total of 800 distinct peaks. The column reports the % of peak assigned to at least one compound generated by the rule sets. (3) The number indicates the diameter