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arXiv · 1505.05874

Combination of genetic crossover and replica-exchange method for conformational search of protein systems

Yoshitake Sakae·Tomoyuki Hiroyasu·Mitsunori Miki·Katsuya Ishii·Yuko Okamoto
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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 $α$-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.

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Yoshitake Sakae, Tomoyuki Hiroyasu, Mitsunori Miki, Katsuya Ishii, Yuko Okamoto. 2015-05-21. Combination of genetic crossover and replica-exchange method for conformational search of protein systems. https://arxiv.org/abs/1505.05874

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