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One of the most widely used techniques for ligand virtual screening is structure-based molecular docking to model the binding pose of a ligand in the binding site of the receptor protein followed by the prediction of binding affinity and/or free energy (Cheng et al., 2012). In contrast to ligand-based approaches that need an initial set of bioactive compounds, the only experimental data required for structure-based docking is the 3D structure of the protein target, although homology models can be used instead (Cavasotto and Phatak, 2009; Ferrara and Jacoby, 2007).
(Cheng et al., 2012) Structure-based virtual screening for drug discovery: a problem-centric review. AAPS J.
(Cavasotto and Phatak, 2009) Homology modeling in drug discovery: current trends and applications. Drug Discov Today.
(Ferrara and Jacoby, 2007) Evaluation of the utility of homology models in high throughput docking. J Mol Model.
(Fang et al., 2016) GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing. PLoS One.