CB-Dock2: improved protein ligand blind docking by integrating cavity detection, docking and homologous template fitting

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 similar to 85% for binding pose prediction (RMSD < 2.0 angstrom), 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/. [GRAPHICS] .

Automated summary

Protein-ligand blind docking is a powerful method for exploring the binding sites of receptors and ligand binding poses. In this study, we improved the docking method by combining CB-Dock with a template-based docking engine, resulting in the development of CB-Dock2. The updated docking server demonstrated better accuracy in binding site identification and binding pose prediction, outperforming other blind docking tools.