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Yang Liu, Xiaocong Yang, Jianhong Gan, Shuang Chen, Zhi‐Xiong Jim Xiao, Yang Cao
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/.
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Liu, Y., Yang, X., Gan, J., Chen, S., Xiao, Z. J., & Cao, Y. (2022). CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting. Nucleic Acids Research, 50(W1), W159–W164. https://doi.org/10.1093/nar/gkac394
Liu, Yang, et al. "CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting." Nucleic Acids Research, vol. 50, no. W1, 2022, pp. W159–W164, https://doi.org/10.1093/nar/gkac394.
Liu, Yang, Xiaocong Yang, Jianhong Gan, Shuang Chen, Zhi‐Xiong Jim Xiao, and Yang Cao. "CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting." Nucleic Acids Research 50, no. W1 (2022): W159–W164. https://doi.org/10.1093/nar/gkac394.
Liu Y., Yang X., Gan J. [и др.] CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting // Nucleic Acids Research. — 2022. — Vol. 50, № W1. — P. W159–W164. — URL: https://doi.org/10.1093/nar/gkac394
@article{liu2022cbdock,
title = {{CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting}},
author = {Yang Liu and Xiaocong Yang and Jianhong Gan and Shuang Chen and Zhi‐Xiong Jim Xiao and Yang Cao},
journal = {Nucleic Acids Research},
year = {2022},
volume = {50},
number = {W1},
pages = {W159--W164},
doi = {10.1093/nar/gkac394},
url = {https://doi.org/10.1093/nar/gkac394}
}TY - JOUR AU - Liu, Yang AU - Yang, Xiaocong AU - Gan, Jianhong AU - Chen, Shuang AU - Xiao, Zhi‐Xiong Jim AU - Cao, Yang TI - CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting JO - Nucleic Acids Research VL - 50 IS - W1 SP - W159 EP - W164 PY - 2022 DA - 2022/05/05 DO - 10.1093/nar/gkac394 UR - https://doi.org/10.1093/nar/gkac394 ER -
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