title: Beware of docking!
abstract: Docking is now routine in virtual screening or lead optimization for drug screening and design. The number of papers related to docking has dramatically increased over the past decade. However, there are many issues to consider when undertaking a docking study. Frequent problems or issues arise, such as the wrong binding site of the target protein, screening using an unsuitable small-molecule database, the choice of docking pose, high dock score but failed in molecular dynamics (MD) simulation, and lack of clarity over whether the compound is an inhibitor or agonist. These problems should be cause for caution and concern before performing docking. Some papers show comprehensive biochemistry experiments but only a simple docking figure. This review presents some evidence to show that the docking might be questionable, despite a high score. In some cases, the accuracy of docking can even change from 0% to 92.66%. Thus, please beware of docking!
authors.affiliation: Human Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan; Research Center for Chinese Medicine and Acupuncture, China Medical University, Taichung 40402, Taiwan; Department of Biomedical Informatics, Asia University, Taichung, 41354, Taiwan. Electronic address: ycc929@MIT.edu.
authors.forename: Yu-Chian
authors.initials: YC
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D015195:Drug Design; D006801:Humans; D008024:Ligands; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation
chemical_list: D008024:Ligands
keywords: computer-aided drug design (CADD); docking; ligand-based drug design; molecular dynamics (MD); occupation time; residence time