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

Authors:
A. A. Albrecht;A. Skaliotis;K. Steinhöfel
Affiliations:
University of Hertfordshire, Science & Technology Research Institute, Hatfield, Herts AL10 9AB, UK;King's College London, Department of Computer Science, Strand, London WC2R 2LS, UK;King's College London, Department of Computer Science, Strand, London WC2R 2LS, UK
Venue:
Computational Biology and Chemistry
Year:
2008

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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