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Protein folding simulations of 2D HP model by the genetic algorithm based on optimal secondary structures

Paper ID Volume ID Publish Year Pages File Format Full-Text
15212 1392 2010 6 PDF Available
Title
Protein folding simulations of 2D HP model by the genetic algorithm based on optimal secondary structures
Abstract

In this paper, based on the evolutionary Monte Carlo (EMC) algorithm, we have made four points of ameliorations and propose a so-called genetic algorithm based on optimal secondary structure (GAOSS) method to predict efficiently the protein folding conformations in the two-dimensional hydrophobic–hydrophilic (2D HP) model. Nine benchmarks are tested to verify the effectiveness of the proposed approach and the results show that for the listed benchmarks GAOSS can find the best solutions so far. It means that reasonable, effective and compact secondary structures (SSs) can avoid blind searches and can reduce time consuming significantly. On the other hand, as examples, we discuss the diversity of protein GSC for the 24-mer and 85-mer sequences. Several GSCs have been found by GAOSS and some of the conformations are quite different from each other. It would be useful for the designing of protein molecules. GAOSS would be an efficient tool for the protein structure predictions (PSP).

Keywords
Protein folding; HP model; Genetic algorithm; Secondary structure
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Protein folding simulations of 2D HP model by the genetic algorithm based on optimal secondary structures
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 34, Issue 3, June 2010, Pages 137–142
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