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

        Author
        Albrecht, A.
        Skaliotis, A.
        Steinhofel, K.
        Attention
        2299/5928
        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<n2/3. The local search procedure employs the stopping criterion (m/δ)D/γ, where m is an estimation of the average number of neighbouring conformations, γ relates to the mean of non-zero differences of the objective function for neighbouring conformations, and 1−δ is the confidence that a minimum conformation has been found. The bound complies with the results obtained for the ten benchmark problems.
        Publication date
        2008
        Published in
        Computational Biology and Chemistry
        Published version
        https://doi.org/10.1016/j.compbiolchem.2008.03.004
        Other links
        http://hdl.handle.net/2299/5928
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