MDock: A Suite for Molecular Inverse Docking and Target Prediction

Molecular docking is commonly used for identification of drug candidates targeting a specified protein of known structure. With the increasing emphasis on drug repurposing over recent decades, molecular inverse docking has been widely applied to prediction of the potential protein targets of a specified molecule. In practice, inverse docking has many advantages, including early supervision of drugs' side effects and toxicity. MDock developed from our laboratory is a protein–ligand docking software based on a knowledge-based scoring function and has numerous applications to lead identification. In addition to its computational efficiency on ensemble docking for multiple protein conformations, MDock is well suited for inverse docking. In this chapter, we focus on introducing the protocol of inverse docking with MDock. For academic users, the MDock package is freely available at http://zoulab.dalton.missouri.edu/mdock.htm .