Figure 3.

Performance differences between CA-CA-guided docking and superimposition over the BM4 dimer cases with rigid-body, medium, large conformational changes. A negative i-RMSD difference means that the top four CA-CA models of a docking case have a lower average i-RMSD than its top four superimposed models. Likewise, the positive difference in Fnat and the negative difference in the number of clashes mean that the top four CA-CA models are better than the top four superimposed models. ‘Rigid-body’, ‘Medium’ and ‘Difficult’ correspond to low, medium and large conformational changes, respectively [21]. The superiority of CA-CA-guided docking over superimposition becomes increasingly clear as the amount of conformational changes on binding increases.