A peptide bond based energy score improve identification of the native structures

Protein structure resolution has lagged far behind sequence determination, as it is often laborious and time-consuming to resolve individual protein structure - more often than not even impossible. For computational prediction, due to the lack of detailed knowledge on the folding driving forces, how to design an energy function is still an open question. Furthermore, an effective criterion to evaluate the performance of the energy function is also lacking. Here we present a novel knowledge-based-energy scoring function, simply considering the interactions of peptide bonds, rather than, as conventionally, the residues or atoms as the most important energy contribution. This energy scoring was evaluated by selecting the X-ray structure from a large number of possibilities. It not only outperforms the best of the previously published statistical potentials, but also has very low computational expense. Besides, we suggest an alternative criterion to evaluate the performance of the energy scoring function, measured by the template modeling score of the selected rank-one. We argue that the comparison should allow for some deviation between the x-ray and predicted structures. Collectively, this accurate and simple energy scoring function, together with the optimized criterion, will significantly advance the computational protein structure prediction.