Basin Hopping as a General and Versatile Optimization Framework for the Characterization of Biological Macromolecules
Figure 4
The 2d grids show projections of BH-sampled minima using two USR-based coordinates (with ctd and cfd as reference points). The projection for the protein with native PDB ID 2ezk is shown in (a), and that for the protein with native PDB ID 1hhp is shown in (b). The grids are color coded with a blue-to-red color scheme to show cells with low-to-high number of minima projected to them. The cell that contains the projection of the native structure is marked with an ×. The range of values of each of the coordinates is estimated as in [40]. Maximum values are based on an extended chain, and minimum values are based on the Flory compact self-excluding model of a chain of amino acids. To improve visualization, the ranges are limited here, and the grids are clipped to allow focusing to regions with some minimal population.
