A replica exchange Monte Carlo algorithm for protein folding in the HP model

BMC Bioinformatics

Table 4 Results for biological and designed sequences

ID	E*	${PERM}_{t_{1}}$	${PERM}_{t_{2}}$	${PERM}_{t_{e x p}}$	ACO-HPPFP-3	REMC_pm	REMC_m
B50-5	-22	5 sec	118 sec	9 sec	820 sec	6 sec	5 sec
B50-7	-17	271 sec	299 sec	284 sec	130 sec	1 sec	2 sec
D-1	-19	3 795 sec	1 sec	2 sec	236 sec	1 sec	1 sec
D-2	-17	9 257 sec	19 356 sec	12 524 sec	951 sec	44 sec	41 sec

Results for PERM and ACO-HPPFP-3 are reproduced from [9]. In all instances, REMC finds optimal conformations relatively easily compared with the other algorithms. REMC does not demonstrate an inherit difficulty folding sequences when conformations involve hydrophobic cores confined to one end of the sequence or the case involving both ends. For every instance, 100 independent runs were conducted of 1 CPU hour each. In cases where not every run reached the same energy value after 1 hour, the expected run-time to reach the energy value shown in the table was calculated using the equation detailed by Parkes and Walser [54].

ISSN: 1471-2105