中文

Journal of Applied Sciences

• Articles • Previous Articles     Next Articles

Prediction of Protein Secondary Structure with an Improved Measure of Information Discrepancy

LI Zhe－qian1,2, LIU Shu-peng1,2, YAN Zhuang-zhi1,2, XIN Yan-fei3   

  1. 1. School of Communication and Information Engineering, Shanghai University,
    2. Institute of Biomedical Engineering, Shanghai University, Shanghai 200072
    3. Zhejiang Academy of Medical Sciences, Hangzhou 310013, Zhejiang
  • Received:2007-09-01 Revised:2007-12-21 Online:2008-03-31 Published:2008-03-31

Abstract: The secondary structure prediction is important in protein structure prediction since protein secondary structure is the basis of the tertiary structure. A method of information discrepancy-FDOD (Function of Degree of Disagreement) was used to predict protein secondary structure in this work. Data were selected from the CB396 database and prediction accuracy was 72.1%. Besides, multiple alignment of PSI-BLAST was used to combine with FDOD, with the prediction accuracy increased to 75.6%. Furthermore, in order to reduce computation complexity, hydrophobic values were introduced to improve the algorithm and the impact factors of hydrophobic values. Long-range interaction is discussed in the prediction of protein secondary structure.

Key words: protein secondary structure prediction, disagreement degree, hydrophobic values, long-range interaction