Programming Environment Based on Distributed Shared Arrays for High-Performance Scientific Computing. - Akira Nomoto; Wataru Kaneko; Tohru Terada; Shugo Nakamura; Kentaro Shimizu (SAINT Workshops, 2004)

Insight of the Signal Motif of GPI-(like)-anchored Proteins by using SVM. - Cao Wei; Kazuya Sumikoshi; Tohru Terada; Shugo Nakamura; Kentaro Shimizu (BIOCOMP, 2006)

ROKU: a novel method for identification of tissue-specific genes. - Koji Kadota; Jiazhen Ye; Yuji Nakai; Tohru Terada; Kentaro Shimizu (BMC Bioinform., 2006)

Computational Protocol for Screening GPI-anchored Proteins. - Cao Wei; Kazuya Sumikoshi; Tohru Terada; Shugo Nakamura; Katsuhiko Kitamoto; Kentaro Shimizu (BICoB, 2009)

Prediction of Carbohydrate-Binding Proteins from Sequences Using Support Vector Machines. - Seizi Someya; Masanori Kakuta; Mizuki Morita; Kazuya Sumikoshi; Cao Wei; Ge Zhenyi; Osamu Hirose; Shugo Nakamura; Tohru Terada; Kentaro Shimizu (Adv. Bioinformatics, 2010)

Multicanonical ab inito QM/MM molecular dynamics simulation of a peptide in an aqueous environment. - Ryota Jono; Yuusuke Watanabe; Kentaro Shimizu; Tohru Terada (J. Comput. Chem., 2010)

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)

Coarse-grained molecular dynamics simulations of protein-ligand binding. - Tatsuki Negami; Kentaro Shimizu; Tohru Terada (J. Comput. Chem., 2014)

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

Tyrosine Kinase Ligand-Receptor Pair Prediction by Using Support Vector Machine. - Masayuki Yarimizu; Cao Wei; Yusuke Komiyama; Kokoro Ueki; Shugo Nakamura; Kazuya Sumikoshi; Tohru Terada; Kentaro Shimizu (Adv. Bioinformatics, 2015)

Development of a prediction system for tail-anchored proteins. - Shunsuke Shigemitsu; Cao Wei; Tohru Terada; Kentaro Shimizu (BMC Bioinform., 2016)

Development of a sugar-binding residue prediction system from protein sequences using support vector machine. - Masaki Banno; Yusuke Komiyama; Cao Wei; Yuya Oku; Kokoro Ueki; Kazuya Sumikoshi; Shugo Nakamura; Tohru Terada; Kentaro Shimizu (Comput. Biol. Chem., 2017)

EXPRORER: Rational Cosolvent Set Construction Method for Cosolvent Molecular Dynamics Using Large-Scale Computation. - Keisuke Yanagisawa; Yoshitaka Moriwaki; Tohru Terada; Kentaro Shimizu (J. Chem. Inf. Model., 2021)

Prediction of protein mononucleotide binding sites using AlphaFold2 and machine learning. - Shohei Yamaguchi; Haruka Nakashima; Yoshitaka Moriwaki; Tohru Terada; Kentaro Shimizu (Comput. Biol. Chem., 2022)

Feedback-AVPGAN: Feedback-guided generative adversarial network for generating antiviral peptides. - Kano Hasegawa; Yoshitaka Moriwaki; Tohru Terada; Cao Wei; Kentaro Shimizu (J. Bioinform. Comput. Biol., 2022)