Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19.

@article{Kozakov2010AchievingRA,
  title={Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19.},
  author={Dima Kozakov and David R. Hall and Dmitri Beglov and Ryan Brenke and Stephen R. Comeau and Yang Shen and Keyong Li and Jiefu Zheng and Pirooz Vakili and Ioannis C. Paschalidis and Sandor Vajda},
  journal={Proteins},
  year={2010},
  volume={78 15},
  pages={3124-30}
}
Our approach to protein-protein docking includes three main steps. First, we run PIPER, a rigid body docking program based on the Fast Fourier Transform (FFT) correlation approach, extended to use pairwise interactions potentials. Second, the 1000 best energy conformations are clustered, and the 30 largest clusters are retained for refinement. Third, the stability of the clusters is analyzed by short Monte Carlo simulations, and the structures are refined by the medium-range optimization method… CONTINUE READING
Highly Influential
This paper has highly influenced a number of papers. REVIEW HIGHLY INFLUENTIAL CITATIONS