Weichenberger Christian X, Sippl Manfred J
Center of Applied Molecular Engineering, University of Salzburg, Jakob Haringerstrasse 5, 5020 Salzburg, Austria.
Structure. 2006 Jun;14(6):967-72. doi: 10.1016/j.str.2006.04.002.
The current protein structure database contains unfavorable Asn/Gln amide rotamers in the order of 20%. Here, we derive a set of self-consistent potential functions to identify and correct unfavorable rotamers. Potentials of mean force for all heavy atoms are compiled from a database of high-resolution protein crystal structures. Starting from erroneous data, a refinement-correction cycle quickly converges to a self-consistent set of potentials. The refinement is entirely driven by the deposited structure data and does not involve any assumptions on molecular interactions or any artificial constraints. The refined potentials obtained in this way identify unfavorable rotamers with high confidence. Since the state of Asn/Gln rotamers is largely determined by hydrogen bond interactions, the features of the respective potentials are of interest in terms of molecular interactions, protein structure refinement, and prediction. The Asn/Gln rotamer assignment is available as a public web service intended to support protein structure refinement and modeling.
当前的蛋白质结构数据库中约有20%的天冬酰胺/谷氨酰胺酰胺旋转异构体处于不利状态。在此，我们推导了一组自洽的势函数来识别和纠正不利的旋转异构体。所有重原子的平均力势是从高分辨率蛋白质晶体结构数据库中汇编得到的。从错误数据开始，一个细化-校正循环能快速收敛到一组自洽的势。细化完全由存入的结构数据驱动，不涉及任何关于分子相互作用的假设或任何人为约束。通过这种方式获得的细化势能够高度可靠地识别不利的旋转异构体。由于天冬酰胺/谷氨酰胺旋转异构体的状态在很大程度上由氢键相互作用决定，因此各自势的特征在分子相互作用、蛋白质结构细化和预测方面具有重要意义。天冬酰胺/谷氨酰胺旋转异构体的分配作为一项公共网络服务提供，旨在支持蛋白质结构的细化和建模。
