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The algorithm has been described previously ( 7 , 8 ).

Like other protein design programs, Rosetta Design has two primary components: an energy function for evaluating the relative favorability of a sequence and an optimization procedure for searching through sequence space.

To allow for relaxation away from the most preferred side chain conformations, additional rotamers are created for buried residues by varying chi1 and chi2 one standard deviation (∼10°) away from the most preferred values.Here are all the one, two, three, and four letter combinations of letters.It's absolutely useless, but your friendly search engine indexed it!In general, when redesigning a naturally occurring protein ∼65% of the residues will mutate.As expected, more sequence variability is seen on the surface of the protein where there are fewer packing constraints.

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