CB-Dock: a web server for cavity detection-guided protein–ligand blind docking

As the number of elucidated protein structures is rapidly increasing, the growing data call for methods to efficiently exploit the structural information for biological and pharmaceutical purposes. Given the three-dimensional (3D) structure of a protein and a ligand, predicting their binding sites a...

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Bibliographic Details
Published in:Acta pharmacologica Sinica 2020-01, Vol.41 (1), p.138-144
Main Authors: Liu, Yang, Grimm, Maximilian, Dai, Wen-tao, Hou, Mu-chun, Xiao, Zhi-Xiong, Cao, Yang
Format: Article
Language:English
Subjects:
Algorithms
Binding Sites
Biomedical and Life Sciences
Biomedicine
Databases, Protein
Drug Design
Immunology
Internal Medicine
Internet
Ligands
Medical Microbiology
Molecular Docking Simulation
Pharmacology/Toxicology
Protein structure
Proteins
Proteins - chemistry
Software
Vaccine
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Summary:As the number of elucidated protein structures is rapidly increasing, the growing data call for methods to efficiently exploit the structural information for biological and pharmaceutical purposes. Given the three-dimensional (3D) structure of a protein and a ligand, predicting their binding sites and affinity are a key task for computer-aided drug discovery. To address this task, a variety of docking tools have been developed. Most of them focus on docking in the preset binding sites given by users. To automatically predict binding modes without information about binding sites, we developed a user-friendly blind docking web server, named CB-Dock, which predicts binding sites of a given protein and calculates the centers and sizes with a novel curvature-based cavity detection approach, and performs docking with a popular docking program, Autodock Vina. This method was carefully optimized and achieved ~70% success rate for the top-ranking poses whose root mean square deviation (RMSD) were within 2 Å from the X-ray pose, which outperformed the state-of-the-art blind docking tools in our benchmark tests. CB-Dock offers an interactive 3D visualization of results, and is freely available at http://cao.labshare.cn/cb-dock/ .
ISSN:1671-4083
1745-7254
DOI:10.1038/s41401-019-0228-6