Stochastic protein folding simulation in the three-dimensional HP-model.
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 (m/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.
Albrecht
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AA
University of Hertfordshire, Science & Technology Research Institute, Hatfield, Herts AL10 9AB, UK.
Skaliotis
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Steinhöfel
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K
D000465:Algorithms; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013269:Stochastic Processes; D013997:Time Factors
D011506:Proteins