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 < n 2 / 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.
Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
