Prediction of β-turns in proteins using neural networks

• Published in: Protein engineering 1989-05, Vol.2 (7), p.521-526
• Main Authors: McGregor, Malcolm J., Flores, Tomas P., Sternberg, Michael J.E.
• Format: Article
• Language: English
• Subjects: Algorithms; Amino Acids; Analytical, structural and metabolic biochemistry; artficial intelligence; artificial intelligence; Biological and medical sciences; Electronic Data Processing; Fundamental and applied biological sciences. Psychology; General aspects, investigation methods; identification; neural networks; predictions; Protein Conformation; Proteins; proteins structure; secondary structure prediction; β-turns
• ISSN: 1741-0126; 0269-2139; 1741-0134; 1460-213X
• DOI: 10.1093/protein/2.7.521

The use of neural networks to improve empirical secondary structure prediction is explored with regard to the identification of the position and conformational class of β-turns, a four-residue chain reversal. Recently an algorithm was developed for β-turn predictions based on the empirical approach of Chou and Fasman using different parameters for three classes (I, II and non-specific) of β-turns. In this paper, using the same data, an alternative approach to derive an empirical prediction method is used based on neural networks which is a general learning algorithm extensively used in artificial intelligence. Thus the results of the two approaches can be compared. The most severe test of prediction accuracy is the percentage of turn predictions that are correct and the neural network gives an overall improvement from 20.6% to 26.0%. The proportion of correctly predicted residues is 71%, compared to a chance level of about 58%. Thus neural networks provide a method of obtaining more accurate predictions from empirical data than a simpler method of deriving propensities.