Predicting Protein Interactions by Brownian Dynamics Simulations
Figure 7
BD sampling and structure refinement of 2SNI. (a) 428,140 compact complexes obtained from BD global sampling. Each gray point represents the center of mass (COM) of one sampled conformation. The receptor of crystal complex is in blue, and near-native conformation obtained after BD sampling is in silver. (b) Representation of near-native conformations obtained from BD sampling (silver, RMSD 11.47 Å), soft potential optimization (yellow, RMSD 2.45 Å) and real potential optimization (red, RMSD 0.27 Å). The receptor and the ligand of crystal complex are in blue and green, respectively.
