2. For each residue in protein, select best rotamer to form protein E0
1. Evaluate energy of a single sidechain with backbone for all rotamers in protein
3. Select all rotamers in E0, and those less than 50 kcal/mol higher in energy to form single excitation set A
An example of the sidechain-main chain evaluation. The backbone of the protein is shown and three rotamers for a specific residue are displayed near the bottom. Each sidechain-main chain evaluation is performed separately.