Previous study shows that the same type of bond lengths and angles fit Gaussian distributions well with small standard deviations on high resolution protein structure data. The mean values of these Gaussian distributions have been widely used as ideal bond lengths and angles in bioinformatics. However, we are not aware of any research work done to evaluate how accurately we can model protein structures with dihedral angles and ideal bond lengths and angles. In this paper, we first introduce the protein structure idealization problem. Then, we develop a fast O(nm/ε) dynamic programming algorithm to find an approximately optimal idealized protein backbone structure according to our scoring function. Consequently, we demonstrate that idealized backbone structures always exist with small changes and significantly better free energy. We also apply our algorithm to refine protein pseudo-structures determined in NMR experiments. © 2012 Springer-Verlag.
CITATION STYLE
Cui, X., Li, S. C., Bu, D., Alipanahi Ramandi, B., & Li, M. (2012). How accurately can we model protein structures with dihedral angles? In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 7534 LNBI, pp. 274–287). https://doi.org/10.1007/978-3-642-33122-0_22
Mendeley helps you to discover research relevant for your work.