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

A. Albrecht, A. Skaliotis, K. Steinhofel

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    22 Citations (Scopus)


    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.
    Original languageEnglish
    Pages (from-to)248-255
    JournalComputational Biology and Chemistry
    Issue number4
    Publication statusPublished - 2008


    • protein folding
    • HP-model
    • landscape analysis
    • stochastic local search
    • simulated annealing


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