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doi: 10.1007/s00167-023-07575-w

Herein, the mh-Tyr crystal structure was also processed by deletion of co-crystallized ligand and water molecules, the addition of polar hydrogen atoms, optimization of hydrogen-bonding network rotation of thiol and hydroxyl hydrogen atoms, tautomerization and protonation states for histidine (His) residue, assignments of Chi flip for asparagine (Asn), glutamine (Gln), and His residues, and optimization of hydrogen atoms in distinct species achieved by the Protein preparation wizard

Importantly, that second cleanse is where the real deep cleaning happens

T.MbiusW.WinklerA.RuhwedelT.WrzosC.RomanelliE.et al (2016)

Machado, C

Here, well dive into their differences to help you decide which one might be right for you