32 citations · 52 across the 5 of their papers we have counts for
5 papers
Combination of genetic crossover and replica-exchange method for conformational search of protein systems
Yoshitake Sakae, Tomoyuki Hiroyasu, Mitsunori Miki +2
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 crossove…
Optimizations of force-field parameters for protein systems with the secondary-structure stability and instability
Yoshitake Sakae, Yuko Okamoto
We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the pro…
Optimizations of protein force fields
Yoshitake Sakae, Yuko Okamoto
In this Chapter we review our works on force fields for molecular simulations of protein systems. We first discuss the functional forms of the force fields and present some extensi…
Secondary-Structure Design of Proteins by a Backbone Torsion Energy
Yoshitake Sakae, Yuko Okamoto
We propose a new backbone-torsion-energy term in the force field for protein systems. This torsion-energy term is represented by a double Fourier series in two variables, the backb…
Optimization of protein force-field parameters with the Protein Data Bank
Yoshitake Sakae, Yuko Okamoto
We propose a novel method to optimize existing force-field parameters for protein systems. The method consists of minimizing the summation of the square of the force acting on each…