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

Albrecht, Andreas A., Skaliotis, A. and Steinhöfel, K. (2008) Stochastic protein folding simulation in the three-dimensional HP-model. Computational Biology and Chemistry, 32 (4) . pp. 248-255. ISSN 1476-9271 [Article] (doi:10.1016/j.compbiolchem.2008.03.004)

Abstract

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<n2/3D<n2/3. The local search procedure employs the stopping criterion (m/δ)D/γ(m/δ)D/γ, where m is an estimation of the average number of neighbouring conformations, γγ relates to the mean of non-zero differences of the objective function for neighbouring conformations, and 1−δ1−δ is the confidence that a minimum conformation has been found. The bound complies with the results obtained for the ten benchmark problems.

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