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

• Published in: Nucleic acids research Vol. 50; no. W1; pp. W159 - W164
• Main Authors: Liu, Yang, Yang, Xiaocong, Gan, Jianhong, Chen, Shuang, Xiao, Zhi-Xiong, Cao, Yang
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 05.07.2022
• Subjects: Algorithms; Binding Sites; GTPase-Activating Proteins - chemistry; Guanine Nucleotide Exchange Factors - chemistry; Ligands; Molecular Docking Simulation; Protein Binding; Proteins - chemistry; Software; Web Server Issue
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkac394

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/. Graphical Abstract Graphical Abstract CB-Dock2 integrates the structure-based and template-based blind docking algorithms.