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

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

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

All numbers correspond to compounds having different InChIs at the connectivity level
(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

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