HybridDock: A Hybrid Protein-Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches

Journal of Chemical Information and Modeling
Sheng-You HuangYi Pan

Abstract

Structure-based molecular docking and ligand-based similarity search are two commonly used computational methods in computer-aided drug design. Structure-based docking tries to utilize the structural information on a drug target like protein, and ligand-based screening takes advantage of the information on known ligands for a target. Given their different advantages, it would be desirable to use both protein- and ligand-based approaches in drug discovery when information for both the protein and known ligands is available. Here, we have presented a general hybrid docking protocol, referred to as HybridDock, to utilize both the protein structures and known ligands by combining the molecular docking program MDock and the ligand-based similarity search method SHAFTS, and evaluated our hybrid docking protocol on the CSAR 2013 and 2014 exercises. The results showed that overall our hybrid docking protocol significantly improved the performance in both binding affinity and binding mode predictions, compared to the sole MDock program. The efficacy of the hybrid docking protocol was further confirmed using the combination of DOCK and SHAFTS, suggesting an alternative docking approach for modern drug design/discovery.

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Citations

Feb 27, 2016·Journal of Chemical Information and Modeling·Andrew Anighoro, Jürgen Bajorath
May 7, 2016·Journal of Chemical Information and Modeling·Heather A CarlsonJames B Dunbar
Jul 6, 2016·Journal of Computer-aided Molecular Design·Ashutosh Kumar, Kam Y J Zhang
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Aug 8, 2018·Journal of Computer-aided Molecular Design·Ashutosh Kumar, Kam Y J Zhang
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Aug 30, 2019·Journal of Computer-aided Molecular Design·Ashutosh Kumar, Kam Y J Zhang
Aug 10, 2018·Frontiers in Chemistry·Ashutosh Kumar, Kam Y J Zhang
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Apr 27, 2021·Journal of Chemical Information and Modeling·Raghuram SrinivasEric C Larson
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Jul 31, 2017··Mohamed Chawki BatoucheKarima Sid

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