Journal
TRENDS IN PHARMACOLOGICAL SCIENCES
Volume 36, Issue 2, Pages 78-95Publisher
ELSEVIER SCIENCE LONDON
DOI: 10.1016/j.tips.2014.12.001
Keywords
docking; computer-aided drug design (CADD); molecular dynamics (MD); ligand-based drug design; residence time; occupation time
Categories
Funding
- National Science Council of Taiwan [NSC102-2325-B039-001, NSC102-2221-E-468-027]
- China Medical University Hospital [DMR-103-096]
- Taiwan Department of Health Clinical Trial and Research Center of Excellence [DOH102-TD-B-111-004]
- Taiwan Department of Health Cancer Research Center of Excellence [MOHW103-TD-B-111-03]
- CMU under the Aim for Top University Plan of the Ministry of Education, Taiwan
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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!
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