关键词: 编码方式, 蛋白质二级结构预测, 支持向量机

Abstract: Coding scheme plays an important role on determining the protein secondary structure prediction.A new comprehensive coding scheme is suggested to use for single-sequence protein secondary structure prediction.The method regards not only the trending factor of every amino acid appearance in protein secondary structure，but also the value of amino acid hydrophobicity，and it uses binary form to express all kinds of amino acid.The different code schemes are used to state the date set of CB513.Then，the theory of Support Vector Machine（SVM） is applied to protein secondary structure prediction.The results show that the prediction accuracy of the new coding scheme are about 1.48% and 10.68% higher than the classical orthogonal matrix and the five coding，respectively.It showes that this coding is more suitable for non-homologous or lower homologous protein structure prediction.

Key words: coding scheme, protein secondary structure prediction, Support Vector Machine（SVM）