Transformation of a design peptide between the α-helix and β-hairpin structures using a helix-strand replica-exchange molecular dynamics simulation

Temperature and pressure denaturation of chignolin: Folding and unfolding simulation by multibaric-multithermal molecular dynamics method

(2013) Hisashi Okumura   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Replica-Permutation Method with the Suwa–Todo Algorithm beyond the Replica-Exchange Method

(2012) Satoru G. Itoh et al.   Journal of Chemical Theory and Computation

Coulomb replica-exchange method: Handling electrostatic attractive and repulsive forces for biomolecules

(2012) Satoru G. Itoh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Folding helical proteins in explicit solvent using dihedral-biased tempering

(2012) C. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Replica-exchange method in van der Waals radius space: Overcoming steric restrictions for biomolecules

(2010) Satoru G. Itoh et al.   JOURNAL OF CHEMICAL PHYSICS

Helix-Hairpin Transitions of a Designed Peptide Studied by a Generalized-Ensemble Simulation

(2010) Satoru G. Itoh et al.   Journal of Chemical Theory and Computation

Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse

(2010) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Optimization of partial multicanonical molecular dynamics simulations applied to an alaninedipeptide in explicit water solvent

(2010) Hisashi Okumura   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Exploring the Universe of Protein Structures beyond the Protein Data Bank

(2010) Pilar Cossio et al.   PLoS Computational Biology

Dissociation aided and side chain sampling enhanced Hamiltonian replica exchange

(2009) Yuguang Mu   JOURNAL OF CHEMICAL PHYSICS

Controlling the secondary-structure-forming tendencies of proteins by a backbone torsion-energy term

(2009) Yoshitake Sakae et al.   MOLECULAR SIMULATION

Partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations

(2008) Hisashi Okumura   JOURNAL OF CHEMICAL PHYSICS

Temperature and Pressure Dependence of Alanine Dipeptide Studied by Multibaric−Multithermal Molecular Dynamics Simulations

(2008) Hisashi Okumura et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computing the stability diagram of the Trp-cage miniprotein

(2008) D. Paschek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA