Journal
BIOINFORMATICS
Volume 19, Issue 13, Pages 1650-1655Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btg223
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Motivation: A new method that uses support vector machines (SVMs) to predict protein secondary structure is described and evaluated. The study is designed to develop a reliable prediction method using an alternative technique and to investigate the applicability of SVMs to this type of bioinformatics problem. Methods: Binary SVMs are trained to discriminate between two structural classes. The binary classifiers are combined in several ways to predict multi-class secondary structure. Results: The average three-state prediction accuracy per protein (Q(3)) is estimated by cross-validation to be 77.07+/-0.26% with a segment overlap (Sov) score of 73.32+/-0.39%. The SVM performs similarly to the 'state-of-the-art' PSIPRED prediction method on a non-homologous test set of 121 proteins despite being trained on substantially fewer examples. A simple consensus of the SVM, PSIPRED and PROFsec achieves significantly higher prediction accuracy than the individual methods.
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