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Heuristic energy landscape paving for protein folding problem in the three-dimensional HP lattice model

Paper ID Volume ID Publish Year Pages File Format Full-Text
15186 1388 2012 10 PDF Available
Title
Heuristic energy landscape paving for protein folding problem in the three-dimensional HP lattice model
Abstract

The protein folding problem, i.e., the prediction of the tertiary structures of protein molecules from their amino acid sequences is one of the most important problems in computational biology and biochemistry. However, the extremely difficult optimization problem arising from energy function is a key challenge in protein folding simulation. The energy landscape paving (ELP) method has already been applied very successfully to off-lattice protein models and other optimization problems with complex energy landscape in continuous space. By improving the ELP method, and subsequently incorporating the neighborhood strategy with the pull-move set into the improved ELP method, a heuristic ELP algorithm is proposed to find low-energy conformations of 3D HP lattice model proteins in the discrete space. The algorithm is tested on three sets of 3D HP benchmark instances consisting 31 sequences. For eleven sequences with 27 monomers, the proposed method explores the conformation surfaces more efficiently than other methods, and finds new lower energies in several cases. For ten 48-monomer sequences, we find the lowest energies so far. With the achieved results, the algorithm converges rapidly and efficiently. For all ten 64-monomer sequences, the algorithm finds lower energies within comparable computation times than previous methods. Numeric results show that the heuristic ELP method is a competitive tool for protein folding simulation in 3D lattice model. To the best of our knowledge, this is the first application of ELP to the 3D discrete space.

► We demonstrate the application of a new optimization technique ELP to the 3D discrete space. ► We propose a heuristic ELP algorithm for 3D HP lattice model. ► The heuristic ELP method combines the improved ELP and a new neighborhood strategy. ► Numeric results show that the proposed method is a competitive tool for protein folding simulation.

Keywords
Protein folding problem; Heuristic algorithm; Energy landscape paving; HP model; Pull moves
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Heuristic energy landscape paving for protein folding problem in the three-dimensional HP lattice model
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 38, June 2012, Pages 17–26
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