Trajectory maps: molecular dynamics visualization and analysis.

ABSTRACT: Molecular dynamics simulations generate trajectories that depict system's evolution in time and are analyzed visually and quantitatively. Commonly conducted analyses include RMSD, R_gyr, RMSF, and more. However, those methods are all limited by their strictly statistical nature. Here we present trajectory maps, a novel method to analyze and visualize protein simulation courses intuitively and conclusively. By plotting protein's backbone movements during the simulation as a heatmap, trajectory maps provide new tools to directly visualize protein behavior over time, compare multiple simulations, and complement established methods. A user-friendly Python application developed for this purpose is presented, alongside detailed documentation for easy usage and implementation. Th

SUBMITTER: Kozic M 

PROVIDER: S-EPMC10789246 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature