2.17 Molecular Docking
The protein structures of interest were retrieved and downloaded from
the Protein Data Bank (PDB) website. For proteins without reported
structures, the three-dimensional structures were predicted using
AlphaFold2. Subsequently, docking grid files were generated using the
Glide Grid module of Schrödinger, which facilitated the molecular
docking studies. A drug library was downloaded from the FDA
(Selleckchem.com) and processed using Schrödinger’s LigPrep module. This
processing included protonation, desalting, hydrogenation, generation of
tautomers and stereoisomers, and energy minimization. The virtual
screening process began with an initial round of high-throughput virtual
screening (HTVS) using Schrödinger’s Glide module. In this stage, the
top 10% of molecules based on their scores were retained for further
analysis. These molecules were then subjected to standard precision (SP)
screening. The top 10% of molecules from the SP screening were further
refined through extra precision (XP) screening.