Docking with MVD

Molecular docking by using Molegro Virtual Docker (MVD) software (Version 6.0, 2013, CLC Bio) was undertaken by introducing PDB files of protein and ligand into the workspace. Before initiation of docking operation, structure of protein and ligand were prepared. Using the detect cavity option, the possible binding pocket(s) on the protein were identified. Reference ligand was used for RMSD calculations. MVD default settings were used including MolDock score [GRID], a grid resolution of 0.30 Å for grid generation, 10 Å radius from the template as the binding site and MolDock SE as the search algorithm. The number of runs was set to 10. After docking, energy minimization and optimization of hydrogen bonds for each pose was done.