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Stochastic protein folding simulation in the three-dimensional HP-model by A.A. Albrecht; A. Skaliotis; K. Steinhöfel is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

What is Stochastic protein folding simulation in the three-dimensional HP-model about?

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/ı) D/ , where m is an estimation of the average number of neighbouring conformations, relates to the mean of non-zero differences of the objective function for neighbouring conformations, and 1ı is the confidence that a minimum conformation has been found. The bound complies with the results obtained for the ten benchmark problems.

Who reads Stochastic protein folding simulation in the three-dimensional HP-model?

Author

A.A. Albrecht; A. Skaliotis; K. Steinhöfel

Publisher

Elsevier Science; Elsevier ; Elsevier Ltd.; Elsevier BV (ISSN 1476-9271)

Published

2008

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)