Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations.
Long time scale molecular dynamics (MD) simulations of biological systems are becoming increasingly commonplace due to the availability of both large-scale computational resources and significant advances in the underlying simulation methodologies. Therefore, it is useful to investigate and develop data mining and analysis techniques to quickly and efficiently extract the biologically relevant information from the incredible amount of generated data. Wavelet analysis (WA) is a technique that can quickly reveal significant motions during an MD simulation. Here, the application of WA on well-converged long time scale (tens of μs) simulations of a DNA helix is described. We show how WA combined with a simple clustering method can be used to identify both the physical and temporal locations of events with significant motion in MD trajectories. We also show that WA can not only distinguish and quantify the locations and time scales of significant motions, but by changing the maximum time scale of WA a more complete characterization of these motions can be obtained. This allows motions of different time scales to be identified or ignored as desired.
Faculty of Chemistry, K. N. Toosi University of Technology , Tehran 1969764499, Iran.
Zahra
Z
Heidari
Department of Medicinal Chemistry, L. S. Skaggs Pharmacy Institute, University of Utah , Salt Lake City, Utah 84112, United States.
Daniel R
DR
Roe
Department of Medicinal Chemistry, L. S. Skaggs Pharmacy Institute, University of Utah , Salt Lake City, Utah 84112, United States.
Rodrigo
R
Galindo-Murillo
Faculty of Chemistry, K. N. Toosi University of Technology , Tehran 1969764499, Iran.
Jahan B
JB
Ghasemi
Department of Medicinal Chemistry, L. S. Skaggs Pharmacy Institute, University of Utah , Salt Lake City, Utah 84112, United States.
Thomas E
TE
Cheatham
D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D058067:Wavelet Analysis
D004247:DNA