EFFICIENT PATTERN COMPARATIVE METHOD FOR SELECTING FUNCTIONALLY IMPORTANT MOTIFS IN PROTEIN SEQUENCES - APPLICATION TO ZINC ENZYMES

We have developed a pattern comparative method for identifying functio nally important motifs in protein sequences. The essence of most stand ard pattern comparative methods is a comparison of patterns occurring in different sequences using an optimized weight matrix. In contrast, our approach is based on a measure of similarity among all the candida te motifs within the same sequence. This method may prove to be partic ularly efficient for proteins encoding the same biochemical function, but with different primary sequences, and when tertiary structure info rmation from one or more sequences is available. We have applied this method to a special class of zinc-binding enzymes known as endopeptida ses,