Dependency of ligand free energy landscapes on charge parameters and solvent models. - Yuko Okamoto; Toshimasa Tanaka; Hironori Kokubo (J. Comput. Aided Mol. Des., 2010)

Ab Initio prediction of protein-ligand binding structures by replica-exchange umbrella sampling simulations. - Hironori Kokubo; Toshimasa Tanaka; Yuko Okamoto (J. Comput. Chem., 2011)

Two-dimensional replica-exchange method for predicting protein-ligand binding structures. - Hironori Kokubo; Toshimasa Tanaka; Yuko Okamoto (J. Comput. Chem., 2013)

Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations. - Kai Liu; Etsurou Watanabe; Hironori Kokubo (J. Comput. Aided Mol. Des., 2017)

Exploring the Stability of Ligand Binding Modes to Proteins by Molecular Dynamics Simulations: A Cross-docking Study. - Kai Liu 033; Hironori Kokubo (J. Chem. Inf. Model., 2017)

Uncovering abnormal changes in logP after fluorination using molecular dynamics simulations. - Kai Liu; Hironori Kokubo (J. Comput. Aided Mol. Des., 2019)

Prediction of ligand binding mode among multiple cross-docking poses by molecular dynamics simulations. - Kai Liu 033; Hironori Kokubo (J. Comput. Aided Mol. Des., 2020)