DeepBSP_Dataset

This is the docking dataset used to build the DeepBSP model. The "Pose" folder<br> contains the structure files. The receptor (Rec.pdb) and the native ligand pose<br> (Lig_native.pdb) pdb files of each complex are stored in the corresponding<br> sub-folder named with the PDB ID of the complex. The ligand poses docked with<br> Autodock Vina of each complex are stored in those pdb files named "Lig_*.pdb".<br> These pdb files are converted from the pdbqt format of Autodock Vina with all<br> nonpolar hydrogens already deleted and can be used to calculate the voxel<br> descriptor by our element voxel calculator. The RMSD of each Vina docked ligand<br> pose with reference to its native binding pose is recorded in those files named<br> "LigDockRMSD_*.dat" in the "RMSD" folder. The score of each docked pose reported<br> by Vina during docking is recorded in those files named "LigVinaScore_*.dat" in<br> the "Score" folder. Please note that for the same ligand pose, there may be<br> small difference between the score reported by Vina during docking and the score<br> reported during rescoring with Vina "scoreonly" method. The complex PDB IDs of<br> the training and the test set of our DeepBSP model are stored in the files named<br> "PDB_TrainSet.dat" and "PDB_TestSet.dat" in the "Index" folder, respectively.<br> The PDB IDs, pose names, and the RMSD values of the poses used in our primary<br> test set are recorded in the "LigPose_TestSet.dat" file, while the corresponding<br> data of our five training subsets are recorded in those "LigPose_TrainSet_*.dat"<br> files. The poses named "Lig_0" in these data files mean the native ligand<br> binding poses of the corresponding complexes. The source code and the parameters<br> of the DeepBSP model and the element voxel calculator are available at<br> https://github.com/BaoJingxiao/DeepBSP.