Deformable complex network for refining low-resolution X-ray structures.

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2015-11-01 Epub Date: 2015-10-27 DOI:10.1107/S139900471501528X

Chong Zhang, Qinghua Wang, Jianpeng Ma

引用次数: 1

Abstract

In macromolecular X-ray crystallography, building more accurate atomic models based on lower resolution experimental diffraction data remains a great challenge. Previous studies have used a deformable elastic network (DEN) model to aid in low-resolution structural refinement. In this study, the development of a new refinement algorithm called the deformable complex network (DCN) is reported that combines a novel angular network-based restraint with the DEN model in the target function. Testing of DCN on a wide range of low-resolution structures demonstrated that it constantly leads to significantly improved structural models as judged by multiple refinement criteria, thus representing a new effective refinement tool for low-resolution structural determination.

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用于精炼低分辨率x射线结构的可变形复杂网络。

在大分子x射线晶体学中，基于低分辨率的实验衍射数据建立更精确的原子模型仍然是一个巨大的挑战。以前的研究使用了可变形弹性网络(DEN)模型来帮助进行低分辨率的结构细化。在本研究中，我们开发了一种新的细化算法，称为可变形复杂网络(DCN)，该算法将一种新的基于角度网络的约束与目标函数中的DEN模型相结合。DCN在大范围低分辨率结构上的测试表明，从多个精化标准来看，DCN不断得到显著的结构模型改进，是一种新的、有效的低分辨率结构确定精化工具。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Acta Crystallographica Section D: Biological Crystallography 生物-晶体学

自引率

13.60%

发文量

审稿时长

3 months

期刊介绍： Acta Crystallographica Section D welcomes the submission of articles covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules or the methods used to determine them. Reports on new structures of biological importance may address the smallest macromolecules to the largest complex molecular machines. These structures may have been determined using any structural biology technique including crystallography, NMR, cryoEM and/or other techniques. The key criterion is that such articles must present significant new insights into biological, chemical or medical sciences. The inclusion of complementary data that support the conclusions drawn from the structural studies (such as binding studies, mass spectrometry, enzyme assays, or analysis of mutants or other modified forms of biological macromolecule) is encouraged. Methods articles may include new approaches to any aspect of biological structure determination or structure analysis but will only be accepted where they focus on new methods that are demonstrated to be of general applicability and importance to structural biology. Articles describing particularly difficult problems in structural biology are also welcomed, if the analysis would provide useful insights to others facing similar problems.