Modeling and active site refinement for G protein-coupled receptors: application to the β-2 adrenergic receptor. - Stanley R. Krystek; S. Roy Kimura; Andrew J. Tebben (J. Comput. Aided Mol. Des., 2006)

Deciphering Cryptic Binding Sites on Proteins by Mixed-Solvent Molecular Dynamics. - S. Roy Kimura; Hai Peng Hu; Anatoly M. Ruvinsky; Woody Sherman; Angelo D. Favia (J. Chem. Inf. Model., 2017)

PairMap: An Intermediate Insertion Approach for Improving the Accuracy of Relative Free Energy Perturbation Calculations for Distant Compound Transformations. - Kairi Furui; Takafumi Shimizu; Yutaka Akiyama; S. Roy Kimura; Yoh Terada; Masahito Ohue (J. Chem. Inf. Model., 2025)

ModBind, a Rapid Simulation-Based Predictor of Ligand Binding and Off-Rates. - William Sinko; Blake Mertz; Takafumi Shimizu; Taisuke Takahashi; Yoh Terada; S. Roy Kimura (J. Chem. Inf. Model., 2025)