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

BMC Bioinformatics

Table 3 Results on 3D benchmark sequences

ID	E*	${PERM}_{t_{e x p}}$	ACO-HPPFP-3	REMC_vshd	REMC_pm	REMC_m
S2-1	-32	-32 (0.1 min)	-32 (30 min)	-32 (0.75 min)	-32 (0.1 min)	-32 (0.1 min)
S2-2	-34	-34 (0.3 min)	-34 (420 min)	-34 (8.1 min)	-34 (0.2 min)	-34 (0.2 min)
S2-3	-34	-34 (0.1 min)	-34 (120 min)	-34 (3.3 min)	-34 (0.1 min)	-34 (0.1 min)
S2-4	-33	-33 (2 min)	-33 (300 min)	-33 (2.2 min)	-33 (0.2 min)	-33 (0.1 min)
S2-5	-32	-32 (0.5 min)	-32 (15 min)	-32 (1.2 min)	-32 (0.1 min)	-32 (0.1 min)
S2-6	-32	-32 (0.1 min)	-32 (720 min)	-32 (1.5 min)	-32 (0.1 min)	-32 (0.1 min)
S2-7	-32	-32 (0.5 min)	-32 (720 min)	-32 (3.9 min)	-32 (0.4 min)	-32 (0.3 min)
S2-8	-31	-31 (0.3 min)	-31 (120 min)	-31 (2.3 min)	-31 (0.2 min)	-31 (0.1 min)
S2-9	-34	-34 (5 min)	-34 (450 min)	-34 (14 min)	-34 (0.7 min)	-34 (0.9 min)
S2-10	-33	-33 (0.01 min)	-33 (60 min)	-33 (2 min)	-33 (0.1 min)	-33 (0.1 min)

Details on runs can be found in the text. Results for PERM and ACO-HPPFP-3 have been reproduced from [9]. All variants of REMC outperform ACO-HPPFP-3. REMC_mand REMC_pmmatch or outperform PERM in 9 of 10 instances. Details of the experimental protocol can be found in the text.

ISSN: 1471-2105