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Molecular docking is the key ingredient of virtual drug screening, a promising and cost-effective approach for finding new drugs. A critical limitation of this approach is the inadequate sampling efficiency of both ligand and/or receptor conformations for finding the lowest energy bound state. To circumvent this limitation, we develop a protein-ligand docking methodology capable of incorporating structural constraints, experimentally derived or theoretically predicted, to improve accuracy and efficiency. We develop a web server with a user-friendly online graphical interface as a platform for accurate and efficient protein-ligand molecule docking.

MedusaDock 2.0: Efficient and Accurate Protein–Ligand Docking With Constraints