Physics Department T38, Technical University Munich, James-Franck-Strasse 1, 85748 Garching, Germany.
Nucleic Acids Res. 2011 Nov;39(21):9118-29. doi: 10.1093/nar/gkr636. Epub 2011 Aug 16.
The awareness of important biological role played by functional, non coding (nc) RNA has grown tremendously in recent years. To perform their tasks, ncRNA molecules typically unite with protein partners, forming ribonucleoprotein complexes. Structural insight into their architectures can be greatly supplemented by computational docking techniques, as they provide means for the integration and refinement of experimental data that is often limited to fragments of larger assemblies or represents multiple levels of spatial resolution. Here, we present a coarse-grained force field for protein-RNA docking, implemented within the framework of the ATTRACT program. Complex structure prediction is based on energy minimization in rotational and translational degrees of freedom of binding partners, with possible extension to include structural flexibility. The coarse-grained representation allows for fast and efficient systematic docking search without any prior knowledge about complex geometry.
近年来，人们对功能性非编码 (nc) RNA 所发挥的重要生物学作用的认识有了极大的提高。为了完成它们的任务，ncRNA 分子通常与蛋白质伴侣结合，形成核糖核蛋白复合物。计算对接技术可以极大地补充它们的结构见解，因为这些技术为整合和完善实验数据提供了手段，而这些数据通常仅限于更大组装体的片段或代表多个空间分辨率水平。在这里，我们提出了一种用于蛋白质-RNA 对接的粗粒度力场，该力场是在 ATTRACT 程序的框架内实现的。复杂结构预测基于配体在旋转和平移自由度中的能量最小化，可能扩展到包括结构灵活性。粗粒度表示允许快速有效地进行系统对接搜索，而无需对复合物几何形状有任何先验知识。
