PL-PatchSurfer2
OpenBabel, Multiconf-Dock and PL-PatchSurfer2
maximum number of conformations for ligand is set to 50 in Multiconf-Dock
Boltzmann-weighted scheme is used for PL-PatchSurfer2
SMILES strings were converted to mol2 file using OpenBabel.
Multiple conformations of a ligand were generated using Multiconf-Dock upto 50.
Molecular surfaces of binding site of 5YGX and all conformations were generated using APBS and the ligands were screend by PL-PatchSurfer. The compounds were ranked by their score.
Although PL-PatchSurfer is one of structure-based methods, using binding pocket,
it does not give a docking pose, rather it just screens complementary of a protein and
ligand using three-dimensional Zernike descriptors. Thus, we do not attach docking poses.
No
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