CB-Dock is a new blind docking method based on cavity detection. A new method of cavity detection based on the curvature value of protein surface has been used in CB-Dock. We have designed the procedure to automaticly identify binding sites, calculate the center and size, and customize the docking box size according to the query ligands, and then perform the molecular docking with AutoDock Vina. Large-scale benchmarking calculations show that docking in small selected sites can enhance the hit ratio and accuracy of blind docking. Accordingly, CB-Dock can improve the facilitation and accuracy as predicting the binding sites of target proteins and the binding poses of query ligands using AutoDock Vina.
|Curvature of protein surface||Cavity detected by clustering||Docking with AutoDock Vina|
Yang Liu, Maximilian Grimm, et al . CB-Dock: a web server for cavity detection-guided protein–ligand blind docking. Acta Pharmacologica Sinica, 2019.