Support vector machines for the classification and prediction of β-turn types

✍ Scribed by Dr Yu-Dong Cai; Xiao-Jun Liu; Xue-biao Xu; Kuo-Chen Chou

• Publisher: John Wiley and Sons
• Year: 2002
• Tongue: English
• Weight: 73 KB
• Volume: 8
• Category: Article
• ISSN: 1075-2617
• DOI: 10.1002/psc.401

✦ Synopsis

Abstract

The support vector machines (SVMs) method is proposed because it can reflect the sequence‐coupling effect for a tetrapeptide in not only a β‐turn or non‐β‐turn, but also in different types of β‐turn. The results of the model for 6022 tetrapeptides indicate that the rates of self‐consistency for β‐turn types I, I′, II, II′, VI and VIII and non‐β‐turns are 99.92%, 96.8%, 98.02%, 97.75%, 100%, 97.19% and 100%, respectively. Using these training data, the rate of correct prediction by the SVMs for a given protein: rubredoxin (54 residues, 51 tetrapeptides) which includes 12 β‐turn type I tetrapeptides, 1 β‐turn type II tetrapeptide and 38 non‐β‐turns reached 82.4%. The high quality of prediction of the SVMs implies that the formation of different β‐turn types or non‐β‐turns is considerably correlated with the sequence of a tetrapeptide. The SVMs can save CPU time and avoid the overfitting problem compared with the neural network method. Copyright © 2002 European Peptide Society and John Wiley & Sons, Ltd.