Secondary structure prediction: combination of three different methods

A combination of three complementary secondary structure predictionmethods is presented. The methods used are the GOR III method,the Homologue method and a new method, the bit pattern method,which is based on hydrophilic/hydrophobic residue patterns.For this purpose a hydropathy scale was developed and is presentedhere. The combination algorithm (Combine method) was designedto take the best results of each method and use their differencesin order to improve the prediction. The combination yields 65.5%correctly predicted residues in three states: -helix (H), ß-strand(E) and aperiodic structure (C) which is an improvement rangingfrom 2.5 to 6.5% compared with the individual methods when testedwith a 67-polypeptide chain database. Seventy-five per centof the regular secondary structure (H and E) runs are correctlylocated and ß-sheet runs are much better located bythe Combine method in comparison to the other methods.