Korostelev Andrei, Bertram Richard, Chapman Michael S
Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4380, USA.
Acta Crystallogr D Biol Crystallogr. 2002 May;58(Pt 5):761-7. doi: 10.1107/s0907444902003402. Epub 2002 Apr 26.
Methods have been developed that further automate the building of macromolecular structures into electron-density maps. The software supports molecular-dynamics real-space refinement of an atomic model to local regions of a map within the context of a popular molecular-modeling program, O [Jones et al. (1991), Acta Cryst. A47, 110-119]. It is implemented as a module to the CNS refinement package [Brünger et al. (1998), Acta Cryst. D54, 905-921], controlled by a graphical user interface and commands executed directly through the molecular-graphics package. The method is illustrated with examples of the building and rebuilding of protein and nucleic acid models in which laborious manual adjustments are avoided. The resulting models show improved convergence during subsequent reciprocal-space refinement. The novel feature of the RSRef2000 software is the combination of simulated-annealing optimization with local real-space refinement, allowing several local minima to be explored quickly and automatically within the context of interactive model building.
已经开发出一些方法，可进一步实现将大分子结构自动构建到电子密度图中的过程。该软件支持在流行的分子建模程序O [琼斯等人（1991年），《晶体学报》A47卷，第110 - 119页] 的框架下，对原子模型进行分子动力学实空间精修，使其适配到图的局部区域。它作为CNS精修软件包 [布鲁格等人（1998年），《晶体学报》D54卷，第905 - 921页] 的一个模块来实现，由图形用户界面控制，并通过分子图形软件包直接执行命令。文中通过蛋白质和核酸模型构建与重建的示例对该方法进行了说明，这些示例避免了费力的手动调整。所得模型在后续的倒易空间精修过程中显示出更好的收敛性。RSRef2000软件的新颖之处在于将模拟退火优化与局部实空间精修相结合，使得在交互式模型构建的背景下能够快速自动地探索多个局部最小值。
