1. CB-Dock2: improved protein-ligand blind docking by integrating cavity detection, docking and homologous template fitting.
- Author
-
Liu Y, Yang X, Gan J, Chen S, Xiao ZX, and Cao Y
- Subjects
- Binding Sites, Ligands, Molecular Docking Simulation, Protein Binding, Software, GTPase-Activating Proteins chemistry, Guanine Nucleotide Exchange Factors chemistry, Algorithms, Proteins chemistry
- Abstract
Protein-ligand blind docking is a powerful method for exploring the binding sites of receptors and the corresponding binding poses of ligands. It has seen wide applications in pharmaceutical and biological researches. Previously, we proposed a blind docking server, CB-Dock, which has been under heavy use (over 200 submissions per day) by researchers worldwide since 2019. Here, we substantially improved the docking method by combining CB-Dock with our template-based docking engine to enhance the accuracy in binding site identification and binding pose prediction. In the benchmark tests, it yielded the success rate of ∼85% for binding pose prediction (RMSD < 2.0 Å), which outperformed original CB-Dock and most popular blind docking tools. This updated docking server, named CB-Dock2, reconfigured the input and output web interfaces, together with a highly automatic docking pipeline, making it a particularly efficient and easy-to-use tool for the bioinformatics and cheminformatics communities. The web server is freely available at https://cadd.labshare.cn/cb-dock2/., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2022
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