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The simulation of the three-dimensional lattice hydrophobic-polar protein folding.

The simulation of the three-dimensional lattice hydrophobic-polar protein folding.

Authors :
Guo, Yu-zhen
Feng, En-min
Source :
Journal of Chemical Physics. 12/21/2006, Vol. 125 Issue 23, p234703. 7p. 6 Diagrams, 3 Charts.
Publication Year :
2006

Abstract

One of the most prominent problems in computational biology is to predict the natural conformation of a protein from its amino acid sequence. This paper focuses on the three-dimensional hydrophobic-polar (HP) lattice model of this problem. The modified elastic net (EN) algorithm is applied to solve this nonlinear programming hard problem. The lattice partition strategy and two local search methods (LS1 and LS2) are proposed to improve the performance of the modified EN algorithm. The computation and analysis of 12 HP standard benchmark instances are also involved in this paper. The results indicate that the hybrid of modified EN algorithm, lattice partition strategy, and local search methods has a greater tendency to form a globular state than genetic algorithm does. The results of noncompact model are more natural in comparison with that of compact model. [ABSTRACT FROM AUTHOR]

Details

Language :
English
ISSN :
00219606
Volume :
125
Issue :
23
Database :
Academic Search Index
Journal :
Journal of Chemical Physics
Publication Type :
Academic Journal
Accession number :
23556211
Full Text :
https://doi.org/10.1063/1.2402162