Parameter tuning support system for docking simulation

When performing docking simulation using DOCK, researchers need to adjust and tune a number of parameters. Also, to perform docking simulation, combination of multiple programs is required. This study focused on the necessity of researchers’ exploration of parameter analytic space and aimed to realize a system that streamline researcher’s trial-and-error parameter-tuing process. Specifically, we have developed a system that automatically sets parameters for docking simulation based on a researcher’s specified “template” composed of execution flow and parameter sets.


Research achievements

  • Takashi Maeno, Susumu Date, Yoshiyuki Kido, and Shinji Shimojo, “Analytic space management for drug design application”, IPSJ Transaction on Bioinformatics, Vol. 47, No. SIG17(TBIO 1), pp.93-104, Nov. 2006.
  • Takashi Maeno, Susumu Date, Yoshiyuki Kido, Ichiro Hasegawa, Shinji Shimojo, “A System Architecture Assisting User Trial-and-Error Process in in-silico Drug Design”, Proceedings of The 7th International Conference on High Performance Computing and Grid in Asia Pacific Region (HPCAsia2004), IEEE CS Press, pp.357-364, Omiya, July 2004.
Related graduation thesis.
  • Takashi Maeno, “試行錯誤的なユーザインタラクションを考慮した創薬シミュレーション支援システムに関する研究”, Graduate School of Information Science and Technology Osaka University, Ph.D dissertation, Jan. 2007. (written in Japanese)