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Protein structure predictions by parallel simulated annealing molecular dynamics using genetic crossover.

Authors
  • Sakae, Yoshitake
  • Hiroyasu, Tomoyuki
  • Miki, Mitsunori
  • Okamoto, Yuko
Type
Published Article
Journal
Journal of computational chemistry
Publication Date
May 01, 2011
Volume
32
Issue
7
Pages
1353–1360
Identifiers
DOI: 10.1002/jcc.21716
PMID: 21246572
Source
Medline
License
Unknown

Abstract

We propose a conformational search method to find a global minimum energy structure for protein systems. The simulated annealing is a powerful method for local conformational search. On the other hand, the genetic crossover can search the global conformational space. Our method incorporates these attractive features of the simulated annealing and genetic crossover. In the previous works, we have been using the Monte Carlo algorithm for simulated annealing. In the present work, we use the molecular dynamics algorithm instead. To examine the effectiveness of our method, we compared our results with those of the normal simulated annealing molecular dynamics simulations by using an α-helical miniprotein. We used genetic two-point crossover here. The conformations, which have lower energy than those obtained from the conventional simulated annealing, were obtained.

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