Protein Engineering vol. 16 no. 9 pp. 659-663, 2003
© 2003 Oxford University Press
A new computational approach for real protein folding prediction
1College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, 2Department of Astronomy and Applied Physics, University of Science and Technology of China, Hefei 230026 and 3Institute of Biophysics, Academia Sinica, Beijing 100101, China
4 To whom correspondence should be addressed. e-mail: cxwang{at}bjut.edu.cn
An effective and fast minimization approach is proposed for the prediction of protein folding, in which the ‘relative entropy’ is used as a minimization function and the off- lattice model is used. In this approach, we only use the information of distances between the consecutive C
atoms along the peptide chain and a generalized form of the contact potential for 20 types of amino acids. Tests of the algorithm are performed on the real proteins. The root mean square deviations of the structures of eight folded target proteins versus the native structures are in a reasonable range. In principle, this method is an improvement on the energy minimization approach.
Received June 25, 2002; revised June 6, 2003; accepted July 29, 2003.