Fig. 2: Trajectory analysis of protein dynamics.
From: Machine learning coarse-grained potentials of protein thermodynamics
Three individual CG trajectories selected from validation MD of Trp-Cage, WW-Domain, and Protein G. Each visualized simulation, colored from purple to yellow, explores the free energy surface, accesses multiple major basins and transitions among conformations. Top panels: 100 states sampled uniformly from the trajectory plotted over CG free energy surface, projected over the first two time-lagged independent components (TICs) for Trp-Cage (a), WW-Domain (b), and Protein G (c). The red line indicates the all-atom equilibrium density by showing the energy level above the free energy minimum with the value of 7.5 kcal/mol. The experimental structure is marked as a red star. Bottom panels: Cα-RMSD of the trajectory with reference to the experimental structure for Trp-Cage (d), WW-Domain (e), and Protein G (f). Source data are provided as a Source data file.
