MFCC Fragmentation Method

While the original MFCC fragmentation method was defined in terms of amino acids it’s straightforward to generalize it to arbitrary molecules. Using our terminology:

1. Form pseudoatoms, letting \(P_I\) be the \(I\)-th pseudoatom

2. The \(I\)-th fragment consists of \(P_I\) and the atoms bonded to it.

The original application of this fragmentation method defined each amino acid of the proteins to be a pseudoatom, which in turn amounted to fragmenting the peptide bonds. This amounts to adding a \(-NH_2\) cap to the \(\alpha\) carbon of the bond and a \(-RCH2\) group to the nitrogen of the peptide bond (R being the side chain of the amino acid the cap is replacing).