MDock: An Ensemble Docking Suite for Molecular Docking, Scoring and In Silico Screening

Abstract

Molecular docking refers to computational methods for the prediction of the binding mode and binding affinity between two molecules. Over decades of development, protein–ligand docking methods have been widely used for in silico screening of molecular libraries for drug candidates, serving as a valuable tool in structure-based drug design. MDock is a protein–ligand docking suite originally released from our laboratory in 2007, which incorporates the iteratively derived knowledge-based scoring function and the ensemble docking method. In this chapter, we describe the methodology and usage of MDock for molecular docking and in silico screening. The MDock suite is freely available to academic users through applications at http://zoulab.dalton.missouri.edu/mdock.htm.