title: HybridDock: A Hybrid Protein-Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches.
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.
authors: Research Support Computing, University of Missouri Bioinformatics Consortium, and Department of Computer Science, University of Missouri , Columbia, Missouri 65211, United States.
authors: Sheng-You
authors: SY
authors: Huang
authors: School of Information Science and Engineering, Central South University , Changsha, Hunan 410083, China.
authors: Min
authors: M
authors: Li
authors: School of Information Science and Engineering, Central South University , Changsha, Hunan 410083, China.
authors: Jianxin
authors: J
authors: Wang
authors: School of Information Science and Engineering, Central South University , Changsha, Hunan 410083, China.|Department of Computer Science, Georgia State University , Atlanta, Georgia 30302, United States.
authors: Yi
authors: Y
authors: Pan
mesh_terms: D008024:Ligands; D062105:Molecular Docking Simulation; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D013329:Structure-Activity Relationship
chemical_list: D008024:Ligands; D011506:Proteins