A computing
system for fragment-based
quantum mechanical calculation of
protein properties is provided. The processor implements a
protein fragmentation module that separates the computer-readable polypeptide sequence into a plurality of data units. For each sub-sequence of three adjacent amino acids in the polypeptide sequence, a first
amino acid, a second
amino acid, and a third
amino acid are identified, each amino acid having a respective backbone comprising an amino group, a carbon, and a carboxyl group, and a
side chain attached to an alpha carbon. The
protein fragmentation module generates data units representing the first alpha carbon, the first carboxyl group, the second amino group, the second alpha carbon, the second carboxyl group, the second
side chain, the third amino group, and the third alpha carbon, and stores the generated data units in a memory.