A new computational approach for real protein folding prediction.
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 Calpha 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.
Lu
Ben Zhuo
BZ
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China.
Wang
Bao Han
BH
Chen
Wei Zu
WZ
Wang
Cun Xin
CX
D000465:Algorithms; D003198:Computer Simulation; D008958:Models, Molecular; D009010:Monte Carlo Method; D017510:Protein Folding; D017434:Protein Structure, Tertiary