Deep Site and Docking Pose (DSDP) is a blind docking strategy accelerated by GPUs, developed by Gao Group. For the site prediction part, several modifications are introduced to PUResNet program. The pose sampling part is similar as AutoDock Vina combined with a number of modifications.
I tried 70000+ different pdbqt structures. Out of the 70000+ structures, 23 pdbqt structures failed to generate any log file or output file. These pdbqt files worked fine with regular Vina.
The three files in site_output (.npy, _feature_generate.txt and *_surface.txt) were succesfully generated, although not log file or docking results.
Below is the print. Attached please find two sets of the ligand and protein files.
DSDP_failed_23.zip
I tried 70000+ different pdbqt structures. Out of the 70000+ structures, 23 pdbqt structures failed to generate any log file or output file. These pdbqt files worked fine with regular Vina. The three files in site_output (.npy, _feature_generate.txt and *_surface.txt) were succesfully generated, although not log file or docking results. Below is the print. Attached please find two sets of the ligand and protein files. DSDP_failed_23.zip
drug discovery ... load 0/23 1HCK_P24941 ... load 1/23 4E26_P15056 ... load 2/23 4E45_Q8IYD8 ... load 3/23 4EOS_P20248 ... load 4/23 5DMJ_P25942 ... load 5/23 5HVW_P01861 ... load 6/23 5YBY_Q6ZMI3 ... load 7/23 6HGT_O75164 ... load 8/23 6K4G_P78356 ... load 9/23 6Y6X_P46776 ... load 10/23 6ZM7_P46776 ... load 11/23 6ZMI_P46776 ... load 12/23 6ZMI_P62750 ... load 13/23 7EM4_P78356 ... load 14/23 7EM5_P78356 ... load 15/23 7F5S_P42766 ... load 16/23 7R4X_P23396 ... load 17/23 8HK1_Q15459 ... load 18/23 AF-P0DP42-F1-model_v4_8 ... load 19/23 AF-Q07699-F1-model_v4_17 ... load 20/23 AF-Q13907-F1-model_v4_2 ... load 21/23 AF-Q3SXY8-F1-model_v4_15 ... load 22/23 AF-Q6UWB1-F1-model_v4_36 ... drug discovery >>> drug discovery !!! Time: 160534.284188