Figure 2: Kinetic basins computed from the BE-META simulations of the WT peptide and its mutants in water. | Scientific Reports

Figure 2: Kinetic basins computed from the BE-META simulations of the WT peptide and its mutants in water.

From: Fusing simulation and experiment: The effect of mutations on the structure and activity of the influenza fusion peptide

Figure 2

In order to compute the kinetic basins the conformations sampled in the BE-META simulations were projected onto the multidimensional space defined by a set of CVs (Radius of gyration, Alphabeta, Alpharmsd, Betarmsd, Hbond, Number of Hydrophobic contacts and Dihedral correlation) and grouped into microstates using the k-means algorithm implemented in METAGUI49. The relative free energy of each cluster was estimated by a weighted histogram procedure and each cluster was then assigned to a kinetic basin, as described in Marinelli et al.50.

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