Perrakis A, Harkiolaki M, Wilson K S, Lamzin V S
Department of Molecular Carcinogenesis, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
Acta Crystallogr D Biol Crystallogr. 2001 Oct;57(Pt 10):1445-50. doi: 10.1107/s0907444901014007. Epub 2001 Sep 21.
The aim of ARP/wARP is improved automation of model building and refinement in macromolecular crystallography. Once a molecular-replacement solution has been obtained, it is often tedious to refine and rebuild the initial (search) model. ARP/wARP offers three options to automate that task to varying extents: (i) autobuilding of a completely new model based on phases calculated from the molecular-replacement solution, (ii) updating of the initial model by atom addition and deletion to obtain an improved map and (iii) docking of a structure onto a new (or mutated) sequence, followed by rebuilding and refining the side chains in real space. A few examples are presented where ARP/wARP made a considerable difference in the speed of structure solution and/or made possible refinement of otherwise difficult or uninterpretable maps. The resolution range allowing complete autobuilding of protein structures is currently 2.0 A, but for map improvement considerable advances over more conventional refinement techniques are evident even at 3.2 A spacing.
ARP/wARP的目的是提高大分子晶体学中模型构建和精修的自动化程度。一旦获得分子置换解，对初始（搜索）模型进行精修和重建往往很繁琐。ARP/wARP提供了三种不同程度自动化该任务的选项：（i）基于从分子置换解计算出的相位自动构建全新模型；（ii）通过添加和删除原子来更新初始模型，以获得改进的电子密度图；（iii）将一个结构对接至新的（或突变的）序列上，随后在真实空间中重建和精修侧链。文中给出了一些示例，展示了ARP/wARP在结构解析速度方面产生了显著差异，和/或使得原本难以精修或无法解释的电子密度图得以精修。目前允许完全自动构建蛋白质结构的分辨率范围是2.0 Å，但即使在3.2 Å的间距下，与更传统的精修技术相比，在电子密度图改进方面也有明显进展。
