An improved statistics-based backbone torsion potential energy for protein loop structure modeling

Accurately modeling protein loops is critical to predicting three-dimensional structures and understanding functions of many proteins. Local interactions between neighboring residue configurations contribute significantly to forming loop conformations. In this paper, we improve our statistical potential energy function (J. Phys. Chem. B 114(5): 1859-1869, 2010) for loop backbone torsion angle conformations by taking influences from the second nearest neighbor effect (SNNE) into consideration. This is based on our study showing that the second nearest neighbors along a protein sequence still have non-negligible influences on the torsion angles conformation of a loop residue while such correlations from further neighbors are much weakened. A biologically meaningful reference state is also introduced. Accuracy and sensitivity enhancements of the new loop torsion potential energy are observed on a decoy set with 4- to 12-residue loop targets.