Fast and accurate method for lattice approximation of protein folds based on dynamic-programming

A dynamic programming method allows one to find the optimal lattice approximation of protein chain folds for a given orientation of the protein relative to the lattice. Construction of the lattice models free of chain self-crossings is facilitated by introducing ‘repulsion’ potentials. The quality of approximation is markedly increased when the links between units are not rigidly fixed. The calculations carried out for proteins of different structural classes demonstrate the efficiency and high accuracy of this method in comparison with other ones.