Fast and accurate protein substructure searching with simulated annealing and GPUs

BMC Bioinformatics

Table 2 ΔAUC relative to SA Tableau Search for 200 queries in the ASTRAL 95% data set.

Method(s)	ΔAUC
SA Tableau Search 4096, SHEBA, SA Tableau Search 8192	0.000
SA Tableau Search 2048	0.0007
SA Tableau Search 1024	0.0012
SA Tableau Seach 512	0.0023
SA Tableau Search 256	0.0039
SA Tableau Search 128	0.0090
QP Tableau Search	0.0160
LOCK2	0.0183
TableauSearch	0.0723
VAST	0.0746
TOPS	0.0756
IR Tableau	0.0761
YAKUSA	0.1034

Difference in AUC relative to SA Tableau Search (4096 restarts) for different methods on the 200 query set against the ASTRAL SCOP 95% sequence identity non-redundant database. The table is sorted by ΔAUC, so that methods with lower AUC than SA Tableau Search (ΔAUC > 0, with p-value < 0.05) are at the bottom of the table. Methods for which there is no statistically significant difference in AUC from SA Tableau Search (4096 restarts) at p-value 0.05 are shown in a single row with ΔAUC = 0.000.

ISSN: 1471-2105