Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland.
J Biomol NMR. 2011 Nov;51(3):265-81. doi: 10.1007/s10858-011-9534-0. Epub 2011 Aug 20.
For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simulation. The methodology and some implementation details of the computation of NMR NOE data, (3)J-couplings and residual dipolar couplings, X-ray scattering intensities from crystals and solutions and neutron scattering intensities used in GROMOS is described and refinement strategies and concepts are discussed using example applications. The GROMOS software allows structure refinement combining different types of experimental data with different types of restraining functions, while using a variety of methods to enhance conformational searching and sampling and the thermodynamically calibrated GROMOS force field for biomolecular simulation.
为了理解细胞过程，必须准确确定生物分子的分子结构。初始模型可以通过结构精修技术得到显著改善。在这里，我们介绍了在 GROMOS 软件中用于生物分子模拟的精修方法和分析技术。本文描述了计算 NMR NOE 数据、（3）J 耦合和残差偶极耦合、晶体和溶液 X 射线散射强度以及用于 GROMOS 的中子散射强度的方法和一些实现细节，并使用示例应用讨论了精修策略和概念。GROMOS 软件允许结合不同类型的实验数据和不同类型的约束函数进行结构精修，同时使用各种方法来增强构象搜索和采样，以及用于生物分子模拟的热力学校准 GROMOS 力场。
