RAPID PROTEIN-STRUCTURE CLASSIFICATION USING ONE-DIMENSIONAL STRUCTURE PROFILES ON THE BIOSCAN PARALLEL COMPUTER

Rapid growth of protein structures database in recent years requires a n effective approach for objective comparison and classification of de posited protein structures. We describe a novel method for structure c omparison and classification based on the alignment of one-dimensional structure profiles. These profiles are obtained by calculating the OC CO pseudodihedral angles (formed by O-C-C-O atoms of carbonyl groups o f consecutive amino acid residues) from protein three-dimensional coor dinates. These angle measurements are then converted into a 24 letter alphabet, and the protein structures are represented by sequences of l etter from this alphabet. The BioSCAN parallel computer, designed for primary sequence alignment, is used to vapidly align and classify thes e one-dimensional structure profiles. We have developed and implemente d weighted scoring matrix to identify structural classes based on comm only found structural motifs. The results of our experiments ave in go od agreement with the traditional protein structure classification sch emes, One-dimensional structure profiles significantly improve efficie ncy of structure comparison and classification.