A Systematic Analysis of the Binding Affinity between the Pim-1 Kinase and Its Inhibitors Based on the MM/3D-RISM/KH Method. - Takeshi Hasegawa; Masatake Sugita; Takeshi Kikuchi; Fumio Hirata (J. Chem. Inf. Model., 2017)

Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations. - Masatake Sugita; Satoshi Sugiyama; Takuya Fujie; Yasushi Yoshikawa; Keisuke Yanagisawa; Masahito Ohue; Yutaka Akiyama (J. Chem. Inf. Model., 2021)

Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations. - Masatake Sugita; Takuya Fujie; Keisuke Yanagisawa; Masahito Ohue; Yutaka Akiyama (J. Chem. Inf. Model., 2022)

Realization of the structural fluctuation of biomolecules in solution: Generalized Langevin mode analysis. - Masatake Sugita; Fumio Hirata (J. Comput. Chem., 2023)

CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides. - Jianan Li; Keisuke Yanagisawa; Masatake Sugita; Takuya Fujie; Masahito Ohue; Yutaka Akiyama (J. Chem. Inf. Model., 2023)

Improving Performance on Replica-Exchange Molecular Dynamics Simulations by Optimizing GPU Core Utilization. - Taisuke Boku; Masatake Sugita; Ryohei Kobayashi 001; Shinnosuke Furuya; Takuya Fujie; Masahito Ohue; Yutaka Akiyama (ICPP, 2024)