The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting
Open accessAbstract
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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Cites
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Accurate prediction of protein structures and interactions using a 3-track network
Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G. R., Wang, J., Cong, Q., Kinch, L. N., Schaeffer, R. D., et al. (2021) · doi:10.1101/2021.06.14.448402 · Cited by 5,549
Highly accurate protein structure prediction for the human proteome
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“Recently, there is an increasingly urgent need of blind docking for the reason that massive protein structures have been determined by AlphaFold2 (5) or RoseTTAFold (6), opening the opportunities to explore new target therapies (7,8).”
BackgroundTrends in the exploitation of novel drug targets
Rask-Andersen, M., Almén, M. S., & Schiöth, H. B. (2011) · Nature Reviews Drug Discovery · doi:10.1038/nrd3478 · Cited by 853
NGL Viewer: a web application for molecular visualization
Rose, A. S., & Hildebrand, P. W. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv402 · Cited by 462
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“Structure-based blind-docking calculations between Ct NmbA and BSH were performed with CB-Dock 2 ( Cavity-detection guided Blind Docking ) [72].”
Metadata
- Authors
- Liu, Y., Yang, X., Gan, J., Chen, S., Xiao, Z.-X., & Cao, Y.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2022-05-24
- Volume
- 50
- Issue
- W1
- Pages
- W159-W164
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W4282913408
- Cited by
- 2,062
- References
- 5
- FWCI
- 160.52
- Type
- journal article
- Language
- en
- Open access
- gold
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