Protein structures are typically retrieved from databases like the Protein Data Bank (PDB) . If the structure of the target protein is not available, homology modeling may be used to predict the structure based on similar proteins. The retrieved or modeled protein structure often requires cleaning, which includes the removal of water molecules, ligands, or ions that are not relevant to the docking study. Additionally, missing atoms or residues in the protein structure need to be added. The protonation states of ionizable residues are adjusted, and the protein structure is subjected to energy minimization to relieve any steric clashes and to stabilize the structure .