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

A A Albrecht, A Skaliotis, K Steinhofel

Research output: Contribution to journalArticlepeer-review

22 Citations (Scopus)


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
Original languageEnglish
Pages (from-to)248 - 255
Number of pages8
Issue number4
Publication statusPublished - Aug 2008


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