Predicting Protein Secondary Structure by a Support Vector Machine Based on a New Coding Scheme

Long-Hui Wang[1] (
Juan Liu[1] (
Yan-Fu Li[2]
Huai-Bei Zhou[1]

[1]School of Computer, Wuhan University, Wuhan 430079, China
[2]International School of Software, Wuhan University, Wuhan 430072, China


Protein structure prediction is one of the most important problems in modern computational biology. Protein secondary structure prediction is a key step in prediction of protein tertiary structure. There have emerged many methods based on machine learning techniques, such as neural networks (NN) and support vector machine (SVM) etc., to focus on the prediction of the secondary structures. In this paper, a new method was proposed based on SVM. Different from the existing methods, this method takes into account of the physical-chemical properties and structure properties of amino acids. When tested on the most popular dataset CB513, it achieved a Q3 accuracy of 0.7844, which illustrates that it is one of the top range methods for protein of secondary structure prediction.

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Japanese Society for Bioinformatics