Protein preparation, protein structure refinement, and energy minimization

Before being used for molecular docking, the selected protein model, LiP, was applied for protein structure refinement and energy minimization using the protein preparation wizard of the Schrödinger suite. The modeled PDB structure file is not appropriately suitable for molecular docking with Glide.^86,87 A standard PDB file often consists of heavy atoms and may contain a co-crystal ligand itself; other components, including water molecules, metal ions, and other cofactors, might be present. The selected protein (LiP) was prepared by exploiting the protein preparation wizard (pre-processed, optimized, and minimized), through the addition of hydrogen atoms, hydrogen bond optimization, and verifying the protonation states of HIS, GLN, and ASN amino acid residues (Schrödinger release 2020-3: Glide, Schrödinger, LLC, New York, NY, 2020).^82,88 Energy minimization was achieved with the help of a default constraint of 0.3 Å RMSD and applying the OPLS 2005 force field.⁸⁵