Combination of genetic crossover and replica-exchange method for conformational search of protein systems
Biomolecules
2015-05-25 v1 Statistical Mechanics
Biological Physics
Abstract
We combined the genetic crossover, which is one of the operations of genetic algorithm, and replica-exchange method in parallel molecular dynamics simulations. The genetic crossover and replica-exchange method can search the global conformational space by exchanging the corresponding parts between a pair of conformations of a protein. In this study, we applied this method to an -helical protein, Trp-cage mini protein, which has 20 amino-acid residues. The conformations obtained from the simulations are in good agreement with the experimental results.
Keywords
Cite
@article{arxiv.1505.05874,
title = {Combination of genetic crossover and replica-exchange method for conformational search of protein systems},
author = {Yoshitake Sakae and Tomoyuki Hiroyasu and Mitsunori Miki and Katsuya Ishii and Yuko Okamoto},
journal= {arXiv preprint arXiv:1505.05874},
year = {2015}
}
Comments
5 pages, 3 figures, Molecular Simulation 41 (2015), in press (the title is changed). arXiv admin note: substantial text overlap with arXiv:1505.05709