Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes. - Nobuyuki Uchikoga; Takatsugu Hirokawa (BMC Bioinform., 2010)

The MEGADOCK project: Ultra-high-speed protein-protein interaction prediction tools on supercomputing environments. - Takehiro Shimoda; Masahito Ohue; Yuri Matsuzaki; Takayuki Fujiwara; Nobuyuki Uchikoga; Takashi Ishida 002; Yutaka Akiyama (BCB, 2013)

MEGADOCK 3.0: a high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments. - Yuri Matsuzaki; Nobuyuki Uchikoga; Masahito Ohue; Takehiro Shimoda; Toshiyuki Sato; Takashi Ishida 002; Yutaka Akiyama (Source Code Biol. Medicine, 2013)