Protein ikincil yapılarını optimal olarak katlayan amino asit çiftleri arasındaki potensiyellerin hesaplanması

We present a method to calculate the pair potentials for folding of protein secondary structures. In the first part of the method necessary training data are generated to compute the potentials. For this purpose a Go-type model and dynamic optimization is used to compute the optimal folding trajectories. A coarse-grained model for a helix and a beta sheet, each consisting of 12 residues has been constructed by representing each amino acid as a bead. The dynamic optimization gives the total optimal force acting on each residue (bead) to fold the protein from an initial configuration to its native state. Next, forces between pairs of residues are derived from this data. This is done by first projecting the optimal residue forces onto the pair-wise directions between residues and expressing these mean forces as (nonlinear) functions of pair-wise distances. We show how to compute the forces between pairs from the mean forces. We next incorporate the derived pair forces into the dynamic model. Thus, for new initial conditions folding is achieved in a predictive way by simulating this model without any need for optimization. We further show that the folding pathways obtained by such ?simple? simulation are similar to folding pathways which can be obtained by the rigorous dynamic optimization. To measure similarity between folds we use MPCA (Multi-way Principal Component Analysis). In addition, mean forces between pairs are presented and analyze