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Protein Engineering vol. 2 no. 3 pp. 185-191, 1988
© 1988 Oxford University Press

RESEARCH-ARTICLE

Secondary structure prediction: combination of three different methods

V. Biou, J.F. Gibrat, J.M. Levin, B. Robson1 and J. Garnier

Laboratoire de Biochimie Physique, INRA, Bat. 433.Université de Paris-Sud, Orsay 91405, France

A combination of three complementary secondary structure prediction methods 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 presented here. The combination algorithm (Combine method) was designed to take the best results of each method and use their differences in order to improve the prediction. The combination yields 65.5% correctly predicted residues in three states: {alpha}-helix (H), ß-strand (E) and aperiodic structure (C) which is an improvement ranging from 2.5 to 6.5% compared with the individual methods when tested with a 67-polypeptide chain database. Seventy-five per cent of the regular secondary structure (H and E) runs are correctly located and ß-sheet runs are much better located by the Combine method in comparison to the other methods.

Keywords: secondary structure prediction/combination of methods/hydropathy scale

Received March 4, 1988; accepted June 7, 1988.


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