Molecular Dynamics and Morphing Protocols for High Accuracy Molecular Docking

Molecular docking is a popular technique to analyse the geometry and the interactions of a ligand in a protein binding site. Flexibility in molecular docking studies is particularly important when the binding pocket is buried inside the protein and the ligand binding is responsible for backbone deformation of the receptor. The major limit is that the most popular docking programs do not consider the conformation changes in the protein of the receptor during the process of binding of the ligand. Here we have considered sampling of molecular dynamics trajectory, and morphing protocol to generate conformers of the receptor, which differs from the available crystal structure. We have also considered the presence of conserved residues to drive ligands toward the binding pocket under blind docking analysis.