  Motivation: Proteins are known to undergo conformational changes in the
course of their functions. The changes in conformation are often attributable
to a small fraction of residues within the protein. Therefore identification of
these variable regions is important for an understanding of protein function.
  Results: We propose a novel method for identification of local conformational
changes in proteins. In our method, backbone conformations are encoded into a
sequence of letters from a 16-letter alphabet (called D2 codes) to perform
structural comparison. Since we do not use clustering analysis to encode local
structures, the D2 codes not only provides a intuitively understandable
description of protein structures, but also covers wide varieties of
distortions. This paper shows that the D2 codes are better correlated with
changes in the dihedral angles than a structural alphabet and a secondary
structure description. In the case of the N37S mutant of HIV-1 protease, local
conformational changes were captured by the D2 coding method more accurately
than other methods. The D2 coding also provided a reliable representation of
the difference between NMR models of an HIV-1 protease mutant.
