Table 4

Listed are the ligands to be used as test cases, the moieties they contain, the ligands found during training which match each moiety, and the total number of proteins used as training examples after post-process culling
Ligand Moiety Training Examples #
ATP Phosphate Chain ATP, 5FA, CH1, CSG, CTP, D3T, 36
(PA O1A O2A O3A PB O1B DCT, DGT, DTP, GTP, TTP
O2B O3B PG O2G O1G O3G)
Ribose ATP, 5GP, ACP, ADN, ADP, AMP, 299
(C1’ C2’ C3’ C4’ O2’ O3’ O4’) ANP, AP0, APC, ATG, C5P, FAD,
GDP, GNP, GTP, NAD, NAP, NDP,
RIB, SAH, SAM, SSA, UDP, ADP,
Adenine ATP, ACO, ACP, ADP, AMP, ANP, 265
(C2 C4 C5 C6 C8 N1 N3 N6 N7 N9) ATG, CMP, COA, FAD, NAD, NAP,
NDP, SAH, SAM, …
Glucose Glucose GLC 85
HEM oxygenated end HEM, DHE, FDE, FDD, HAS, HCO, 316
(O1A O2A CGA CBA CAA C2A HDD, HEA, HEB, HEC, HEV, HFM,
CMA C3A C1A CHA C4A NA CHB) HIF, VEA, VER, …
non-oxygenated end (1) HEM, HDD, HDM, HEA, HEB, 318
(CHB C1B NB CMB C2B C4B HEC, HFM, HKL, …
CHC C3B CAB CBB)
non-oxygenated end (2) HEM, HDD, HDM, HEA, HEB, 318
(CHD C4C NC CAC C3C C1C HEC, HFM, HKL, …
CHC C2C CBC CMC)
DHT (O3 C1-10 C19) DHT, AE2, AND, C0R, CLR, CPQ, 40
DXC, FFA, HC2, HCY, STR, TES …
(O17 C8 C9 C11-18) DHT, AE2, AND, ASD, EST, FFA, 22
TES, WZA …

Cipriano et al.

Cipriano et al. BMC Bioinformatics 2012 13:314   doi:10.1186/1471-2105-13-314

Open Data