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ISSN 1672-9145 Acta Biochim Biophys Sin 2005, 37(3): 167–172 CN 31-1940/Q

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Protein Secondary Structure Prediction Using Dynamic Programming

Jing ZHAO^1,2,3, Pei-Ming SONG¹, Qing FANG¹, and Jian-Hua LUO^1,2*

¹School of Life Science & Technology, Shanghai Jiaotong University, Shanghai 200240, China;

²Shanghai Center for Bioinformation and Technology, Shanghai 200235, China;

³Logistical Engineering University, Chongqing 400016, China

Abstract In the present paper, we describe how a directed graph was constructed and then searched for the optimum path using a dynamic programming approach, based on the secondary structure propensity of the protein short sequence derived from a training data set. The protein secondary structure was thus predicted in this way. The average three-state accuracy of the algorithm used was 76.70%.

Key words directed graph; dynamic programming approach; protein secondary structure

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Received: October 18, 2004 Accepted: January 17, 2005

This work was supported by the grants from the National High Technology Research and Development Program of China (No. 2002AA234021), the National Basic Research Program of China (No. 2002 CB 512800), the Science and Technology Committee of Shanghai (No. K02D 105501), and the Corporation Project of Shanghai Jiaotong University and Shanghai Second Medical University

*Corresponding author: Tel, 86-21-54742963; E-mail, [email protected]