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)

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)

QUBO Problem Formulation of Fragment-Based Protein-Ligand Flexible Docking. - Keisuke Yanagisawa; Takuya Fujie; Kazuki Takabatake; Yutaka Akiyama (Entropy, 2024)