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SCWRL program for mutant modelling

I have a question regarding SCWRL4 program for prediction of protein side-side chain conformation. Why we have to do mutant modeling of our mutated amino acid as we perform substitution from a particular base to another of a given preptide? Does the protein change structure when we do substitution so that we have to use SCWRL4 for predicting the side chain conformation for a given protein backbone ?

alignment

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