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Population-based local search for protein folding simulation in the MJ energy model and cubic lattices

Paper ID Volume ID Publish Year Pages File Format Full-Text
15296 1401 2009 12 PDF Available
Title
Population-based local search for protein folding simulation in the MJ energy model and cubic lattices
Abstract

We present experimental results on benchmark problems in 3D cubic lattice structures with the Miyazawa–Jernigan energy function for two local search procedures that utilise the pull-move set: (i) population-based local search (PLS) that traverses the energy landscape with greedy steps towards (potential) local minima followed by upward steps up to a certain level of the objective function; (ii) simulated annealing with a logarithmic cooling schedule (LSA). The parameter settings for PLS are derived from short LSA-runs executed in pre-processing and the procedure utilises tabu lists generated for each member of the population. In terms of the total number of energy function evaluations both methods perform equally well, however, PLS has the potential of being parallelised with an expected speed-up in the region of the population size. Furthermore, both methods require a significant smaller number of function evaluations when compared to Monte Carlo simulations with kink-jump moves.

Keywords
Protein folding simulation; Miyazawa–Jernigan energy function; Landscape analysis; Stochastic local search; Simulated annealing; Tabu search
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 33, Issue 4, August 2009, Pages 283–294
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us