Figure 2.

Flow chart of the flexible docking method. In our flexible docking approach using the PRS model, we generate an ensemble of receptor conformations through several steps: (i) sequentially exerting random external force on each single-residue of the CVN mutants, (ii) calculating the response fluctuation vector using the PRS method, (iii) constructing the low-resolution deformed structures (i.e., backbone) using the response vectors after each single residue perturbation, (iv) clustering the perturbed conformations using the k-clustering method, and (v) all-atom minimization of each clustered conformation. Once the MRCs ensemble is completed, we perform a docking simulation using the RosettaLigand option in the ROSETTA package for each minimized structure in the ensemble. (vi) Lastly, the binding energies of the CVN-dimannose complexes with the lowest Ligsum score are evaluated using X-Score. To see this figure in color, go online.