Stochastic protein folding simulation in the three-dimensional HP-model

TY - JOUR

T1 - Stochastic protein folding simulation in the three-dimensional HP-model

AU - Albrecht, A A

AU - Skaliotis, A

AU - Steinhofel, K

PY - 2008/8

Y1 - 2008/8

N2 - We present results from three-dimensional protein folding simulations in the HP-model on ten benchmark problems. The simulations are executed by a simulated annealing-based algorithm with a time-dependent cooling schedule. The neighbourhood relation is determined by the pull-move set. The results provide experimental evidence that the maximum depth D of local minima of the underlying energy landscape can be upper bounded by D <n(2/3). The local search procedure employs the stopping criterion (In/delta)(D/gamma) where m is an estimation of the average number of neighbouring conformations, gamma relates to the mean of non-zero differences of the objective function for neighbouring conformations, and 1-delta is the confidence that a minimum conformation has been found. The bound complies with the results obtained for the ten benchmark problems. (c) 2008 Elsevier Ltd. All rights reserved

AB - We present results from three-dimensional protein folding simulations in the HP-model on ten benchmark problems. The simulations are executed by a simulated annealing-based algorithm with a time-dependent cooling schedule. The neighbourhood relation is determined by the pull-move set. The results provide experimental evidence that the maximum depth D of local minima of the underlying energy landscape can be upper bounded by D <n(2/3). The local search procedure employs the stopping criterion (In/delta)(D/gamma) where m is an estimation of the average number of neighbouring conformations, gamma relates to the mean of non-zero differences of the objective function for neighbouring conformations, and 1-delta is the confidence that a minimum conformation has been found. The bound complies with the results obtained for the ten benchmark problems. (c) 2008 Elsevier Ltd. All rights reserved

U2 - 10.1016/j.compbiolchem.2008.03.004

DO - 10.1016/j.compbiolchem.2008.03.004

M3 - Article

SN - 1476-928X

VL - 32

SP - 248

EP - 255

JO - COMPUTATIONAL BIOLOGY AND CHEMISTRY

JF - COMPUTATIONAL BIOLOGY AND CHEMISTRY

IS - 4

ER -