超並列計算によるタンパク質ドッキングソフトウェア

参考文献

MEGADOCK 4.0

• Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama. MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers, Bioinformatics, 30(22): 3281-3283, 2014.
  

旧バージョンなど

• Masahito Ohue, Yuri Matsuzaki, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama. MEGADOCK: An all-to-all protein-protein interaction prediction system using tertiary structure data, Protein and Peptide Letters, 21(8): 766-778, 2014.
  
• Takehiro Shimoda, Takashi Ishida, Shuji Suzuki, Masahito Ohue, Yutaka Akiyama. MEGADOCK-GPU: An accelerated protein-protein docking calculation on GPUs, In Proc. ACM-BCB 2013 (ParBio workshop 2013), 884-890, 2013.
  
• Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Takehiro Shimoda, Toshiyuki Sato, Takashi Ishida, Yutaka Akiyama. MEGADOCK 3.0: A high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments, Source Code for Biology and Medicine, 8(1): 18, 2013.
  
• Masahito Ohue, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama. Improvement of the Protein-Protein Docking Prediction by Introducing a Simple Hydrophobic Interaction Model: an Application to Interaction Pathway Analysis. Lecture Note in Bioinformatics 7632 (In Proc. of PRIB 2012), 178-187, Springer Heidelberg, 2012.
  
• Takehiro Shimoda, Shuji Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama. Protein-Protein Docking on Hardware Accelerators: Comparison of GPU and MIC Architectures, BMC Systems Biology, 9(Suppl 1): S6, 2015.

応用事例

• Yuri Matsuzaki, Masahito Ohue, Nobuyuki Uchikoga, Yutaka Akiyama. Protein-protein interaction network prediction by using rigid-body docking tools: application to bacterial chemotaxis, Protein and Peptide Letters, 21(8): 790-798, 2014.
• Masahito Ohue, Yuri Matsuzaki, Takehiro Shimoda, Takashi Ishida, Yutaka Akiyama. Highly Precise Protein-Protein Interaction Prediction Based on Consensus Between Template-Based and de Novo Docking Methods, BMC Proceedings, 7(Suppl 7): S6, 2013.
• Masahito Ohue, Yuri Matsuzaki, Yutaka Akiyama. Docking-calculation-based Method for Predicting Protein-RNA Interactions, Genome Informatics, 25(1): 25-39, 2011.