The combination of three secondary structures and 21 amino acid types (20 normal amino acids and 1 pre-proline) makes total of 63 types of potentials. The residue-wise secondary-structure functions are applied on each residue based on predicted local secondary structure information. The local structures for each residue—either helix, extended sheet, or coil—are predicted from amino acid sequence using PSIPRED program [24]. This protocol, however, might be limited to globular proteins for which reliable predictions are available