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Article ID: 359 - Last Modified: January 3, 2011

The Protein Preparation Wizard warns me that there are residues with missing atoms and that I should add the side-chains using Prime. I do not have Prime installed. What should I do?

If the residues with missing atoms are not near the binding site or region of interest, you probably do not need to add them. If the residues are in an important region, you could add them, but be very cautious. Since you don't know the right conformation for the residue, it may be wise to create a few plausible conformations for the residue in order to create a few alternate protein structures for downstream use. Adding the residues in some default conformation is possibly worse than not adding them at all.

Keywords: protein preparation, missing atoms, Prime, Maestro

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