Optimizing substitution matrices by separating score distributions. - Yuichiro Hourai; Tatsuya Akutsu; Yutaka Akiyama (Bioinform., 2004)

Network-aware Data mMapping on Parallel Molecular Dynamicas. - Yuichiro Hourai; Akira Nishida; Yoshio Oyanagi (ICPADS (1), 2005)

High Performance 3D Convolution for Protein Docking on IBM Blue Gene. - Akira Nukada; Yuichiro Hourai; Akira Nishida; Yutaka Akiyama (ISPA, 2007)

Development of an Affinity Evaluation and Prediction System by Using the Shape complementarity Characteristic between proteins. - Koki Tsukamoto; Tatsuya Yoshikawa; Yuichiro Hourai; Kazuhiko Fukui; Yutaka Akiyama (J. Bioinform. Comput. Biol., 2008)

Improving the Accuracy of an Affinity Prediction Method by Using Statistics on Shape Complementarity between Proteins. - Tatsuya Yoshikawa; Koki Tsukamoto; Yuichiro Hourai; Kazuhiko Fukui (J. Chem. Inf. Model., 2009)