https://www.abbs.info
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ISSN
1672-9145
Acta Biochim Biophys Sin
2005, 37(3): 167–172
CN 31-1940/Q
Protein Secondary Structure Prediction Using
Dynamic Programming
Jing ZHAO1,2,3, Pei-Ming SONG1, Qing FANG1,
and Jian-Hua LUO1,2*
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]