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

A novel method for identification of local conformational changes in proteins