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.