Folding small proteins via annealing stochastic approximation Monte Carlo

Cheon, Sooyoung; Liang, Faming

doi:10.1016/j.biosystems.2011.05.015

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Folding small proteins via annealing stochastic approximation Monte Carlo

Cheon, Sooyoung;
Liang, Faming

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6

초록

Recently, the stochastic approximation Monte Carlo algorithm has been proposed by Liang et al. (2007) as a general-purpose stochastic optimization and simulation algorithm. An annealing version of this algorithm was developed for real small protein folding problems. The numerical results indicate that it outperforms simulated annealing and conventional Monte Carlo algorithms as a stochastic optimization algorithm. We also propose one method for the use of secondary structures in protein folding. The predicted protein structures are rather close to the true structures. (C) 2011 Elsevier Ireland Ltd. All rights reserved.

키워드

Protein folding; Secondary structure; Markov chain Monte Carlo; Annealing stochastic approximation Monte Carlo; SECONDARY STRUCTURE; GLOBULAR-PROTEINS; FOLDED STATES; ALGORITHM; OPTIMIZATION; PREDICTION; KINETICS; MODEL; NUCLEATION; PATHWAYS

제목: Folding small proteins via annealing stochastic approximation Monte Carlo

저자: Cheon, Sooyoung; Liang, Faming

DOI: 10.1016/j.biosystems.2011.05.015

발행일: 2011-09

유형: Article

저널명: BioSystems

권: 105

호: 3

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