BACKGROUND A commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central α-carbon coordinates. RESULTS We employ advances in virtual reality to address the problem. The outcome is a 3D visualisation based technique where all the heavy backbone and side chain atoms are treated on equal footing, in terms of the Cα coordinates. Each heavy atom is visualised on the surfaces of a different two-sphere, that is centered at another heavy backbone and side chain atoms. In particular, the rotamers are visible as clusters, that display a clear and strong dependence on the underlying backbone secondary structure. CONCLUSIONS We demonstrate that there is a clear interdependence between rotameric states and secondary structure. Our method easily detects those atoms in a crystallographic protein structure which are either outliers or have been likely misplaced, possibly due to radiation damage. Our approach forms a basis for the development of a new generation, visualization based side chain construction, validation and refinement tools. The heavy atom positions are identified in a manner which accounts for the secondary structure environment, leading to improved accuracy.

中文翻译：

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蛋白质重原子结构重建的三维可视化方法。

背景技术在结构蛋白研究中普遍出现的问题是，根据中心α-碳坐标的知识确定所有重原子的位置。结果我们利用虚拟现实技术来解决该问题。结果是一种基于3D可视化的技术，其中所有重链和侧链原子均根据Cα坐标以平等的基础进行处理。每个重原子都在不同的两个球的表面上可视化，该球以另一个重骨架和侧链原子为中心。尤其是，旋转异构体以簇的形式可见，显示出对基础骨干二级结构的清晰而强烈的依赖性​​。结论我们证明了在旋转异构状态和二级结构之间存在明显的相互依赖性。我们的方法可以很容易地检测出晶体蛋白质结构中的那些原子，这些原子要么是异常原子，要么可能是由于辐射损伤而错位的原子。我们的方法为开发新一代基于可视化的侧链构建，验证和优化工具奠定了基础。通过考虑二级结构环境的方式来识别重原子位置，从而提高了准确性。