open access

https://hdl.handle.net/2115/69978

Two Perturbations for Geometry Optimization of Off-Lattice Bead Protein Models

英語

potential energy

2017-08

Wiley

Molecular Informatics

36(8)

1600096

Referring to the optimization algorithm previously developed for atomic clusters, the present author develops an efficient method for geometry optimization of a coarse‐grained protein model expressed with two kinds of beads (hydrophilic and hydrophobic ones). In the method, two types of geometrical perturbations, center‐directed bead move and one bead rotation, are used to explore new configurations and local optimizations are performed after the perturbations. The center‐directed bead move is used for hydrophobic beads and the one bead rotation is performed for both hydrophobic and hydrophilic beads. The optimization method was applied to protein models consisting of 13, 20, 21, and 34 beads. The present method produced the global minima of the 13‐, 21‐, and 34‐bead models reported in the literature and updated the lowest energies of the protein models with 20 beads. These results indicate that the present method is efficient for searching for optimal structures of proteins.

学術雑誌論文

Accepted Manuscript

This is the peer reviewed version of the following article: http://onlinelibrary.wiley.com/doi/10.1002/minf.201600096/full, which has been published in final form at 10.1002/minf.201600096. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.

1868-1743

AA12449791