DeepBSP_Dataset

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