Docking pose rescoring using PL-PatchSurfer
AutoDock Vina 1.1.2
PL-PatchSurfer2
Gasteiger charges
Receptor preparation: UCSF Chimera was used to remove hetero atoms in 5YGX PDB file
prepare_receptor4.py was used to generate receptor PDBQT file
Ligand preparation: SMILES string of each ligand was converted to mol2 file using OpenBabel
The mol2 files were further converted to PDBQT file using prepare_ligand4.py
AutoDockVina - Num_modes=20, energy_window=20, size_x, size_y, and size_y were set to 25, center_x, center_y, center_z were determined by the geometrical center of co-crystalized ligand in 5YGX. // PL-PatchSurfer - Molecular surfaces of 20 docking poses of each ligand and receptor binding pocket were generated using APBS.
Rescoring docking pose from AutoDock Vina by PL-PatchSurfer. Lowest 5 conformations were selected and submitted
Yes
No