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Zbl 1159.92016
Albrecht, A.A.; Skaliotis, A.; Steinhöfel, K.
Stochastic protein folding simulation in the three-dimensional HP-model. (English)
[J] Comput. Biol. Chem. 32, No. 4, 248-255 (2008). ISSN 1476-9271

Summary: We present results from three-dimensional protein folding simulations in the hydro\-phobic-hydrophilic (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.

MSC 2000:: *92C40 Biochemistry, etc.
92-08 Computational methods (appl. to natural sciences)

Keywords: HP-model; landscape analysis; stochastic local search; simulated annealing

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Zentralblatt MATH Berlin [Germany]