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

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 u...

Celý popis

Uloženo v:
Podrobná bibliografie
Vydáno v:Nucleic acids research Ročník 50; číslo W1; s. W159 - W164
Hlavní autoři: Liu, Yang, Yang, Xiaocong, Gan, Jianhong, Chen, Shuang, Xiao, Zhi-Xiong, Cao, Yang
Médium: Journal Article
Jazyk:angličtina
Vydáno: England Oxford University Press 05.07.2022
Témata:
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
On-line přístup:Získat plný text
Tagy: Přidat tag
Žádné tagy, Buďte první, kdo vytvoří štítek k tomuto záznamu!
Popis
Shrnutí: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.
Bibliografie:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
The authors wish it to be known that, in their opinion, the first three authors should be regarded as Joint First Authors.
ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkac394