Presto(protein Engineering Simulator): A Vectorized Molecular Mechanics Program for Biopolymers. - Kenji Morikami; Takahisa Nakai; Akinori Kidera; Minoru Saito; Haruki Nakamura (Comput. Chem., 1992)

Linear response theory in dihedral angle space for protein structural change upon ligand binding. - Satoshi Omori; Sotaro Fuchigami; Mitsunori Ikeguchi; Akinori Kidera (J. Comput. Chem., 2009)

SAHG, a comprehensive database of predicted structures of all human proteins. - Chie Motono; Junichi Nakata; Ryotaro Koike; Kana Shimizu; Matsuyuki Shirota; Takayuki Amemiya; Kentaro Tomii; Nozomi Nagano; Naofumi Sakaya; Kiyotaka Misoo; Miwa Sato; Akinori Kidera; et al. (Nucleic Acids Res., 2011)

PSCDB: a database for protein structural change upon ligand binding. - Takayuki Amemiya; Ryotaro Koike; Akinori Kidera; Motonori Ota (Nucleic Acids Res., 2012)

Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase. - Yasuhiro Matsunaga; Hiroshi Fujisaki; Tohru Terada; Tadaomi Furuta; Kei Moritsugu; Akinori Kidera (PLoS Comput. Biol., 2012)

Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling. - Kei Moritsugu; Tohru Terada; Akinori Kidera (PLoS Comput. Biol., 2014)

Binding and Unbinding Pathways of Peptide Substrates on the SARS-CoV-2 3CL Protease. - Kei Moritsugu; Toru Ekimoto; Mitsunori Ikeguchi; Akinori Kidera (J. Chem. Inf. Model., 2023)