Are alternate side-chain conformations considered when using the Protein Preparation Wizard?

No, the Protein Preparation Wizard only considers one conformation, as do almost all of our programs. If alternate positions might be relevant for binding, we suggest preparing a second conformation of the receptor with the alternate side-chain positions. If your protein has both sets of coordinates, you can switch to the alternate positions in Maestro by selecting the atoms that have alternate positions, then right-clicking and choosing Switch Alternate Positions from the shortcut menu. From Suite 2012, you can select the alternate positions you want to use in the Protein Preparation - Problems dialog box.

Keywords: protein preparation, alternate side-chain conformations, Maestro, alternate coordinates

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