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Does Rosetta have standalone alanine scanning protocol? I have known that alanine scanning is available on the web.
Alanine scanning is implemented in RosettaScripts. See these threads:
http://www.rosettacommons.org/content/how-define-specific-residues-alascan
http://www.rosettacommons.org/content/it-possible-do-alanine-scanning-rosetta-321