Paper Citing NAMD - Abstract
Ito, M.; Nishikawa, T.; Nagashima, U.
Replica exchange molecular dynamics toolkit for drug-receptor docking
NANOTECH 2003, VOL 1, 36-39, 2003
Although the protein flexibility plays an important role in the drug-receptor dockin process, the treatment of protein structural fluctuations remains a major challenge to docking simulations. To deal with this problem, we have developed a new software framework which enhances the efficiency of conformational sampling by replica exchange molecular dynamics (REMD) method. The effectiveness of the method was examined with the polypeptide molecule and it was shown that the trajectories in REMD method explored the energy region faster than the Monte Carlo moves in the ordinary replica exchange method. Our toolkit employs object-oriented design to mask the complexity associated with biomolecules and parallelization, and to facilitate the adaptation to other software component.
