A New Minimization Method for Real Protein Folding Prediction

A new effective and fast minimization approach is proposed for the prediction of protein folding, in which the“relative entropy”is used as minimization function. Unlike the energy minimization method, the essence of this approach is to search the conformation with high occupation probability, which corresponds to the state with low free energy instead of low energy. The off-lattice model is used, and the prediction just focuses on the frame of the main chain of protein. In this approach, only the distances between the consecutive Cα atoms along the peptide chain and a generalized form of the contact potential for 20 types of amino acids are used. Tests of the prediction algorithm are performed on real proteins with the initial structure fully denatured. The root mean square deviations (RMSD) of the structures of four folded target proteins versus the native structures are from 5 to 7. The advantage of this approach is its simple potential function and fast performance. Moreover, it can be considered as an improvement on the energy minimization method in principle.