Journal
COMPUTATIONAL BIOLOGY AND CHEMISTRY
Volume 34, Issue 3, Pages 137-142Publisher
ELSEVIER SCI LTD
DOI: 10.1016/j.compbiolchem.2010.04.002
Keywords
Protein folding; HP model; Genetic algorithm; Secondary structure
Funding
- National Natural Science Foundation of China [10974061]
- Program for Innovative Research Team of the Higher Education in Guangdong [06CXTD005]
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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 (GAUSS) 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 GAUSS 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 GAUSS and some of the conformations are quite different from each other. It would be useful for the designing of protein molecules. GAUSS would be an efficient tool for the protein structure predictions (PSP). (C) 2010 Elsevier Ltd. All rights reserved.
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