In the MFCC scheme , proteins are partitioned into single amino acid fragments by cutting the peptide bonds. To restore dangling valences, the cut bonds are capped with ACE and NME groups (see Fig. ). Disulfide bridges are cut at the S-S bond and capped with methyl sulfide groups . The capping groups of neighboring fragments are joined to form a cap molecule, which can be subtracted to correct of the effects of the capping groups. To approximate the total energy of a protein containing N amino acids the sum over all energies of the cap molecules, formed by combining the corresponding ACE and NME groups, is subtracted from the sum over all energies of the capped fragments, i.e.,