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

Abstract

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.

Size‐guided multi‐seed heuristic method for geometry optimization of clusters: Application to benzene clusters

“…However, other algorithms, such as evolutionary algorithm and basin‐hopping algorithm, are also used as strategies of geometrical improvements. It would be very interesting to apply SGMS‐HMGP to other systems, multicomponent Lennard‐Jones atomic clusters, water clusters, and off‐lattice protein models . These applications are helpful to evaluate the size‐guided multi‐seed algorithm.…”