Stereochemical Assessment of (φ,ψ) Outliers in Protein Structures Using Bond Geometry-Specific Ramachandran Steric-Maps.,Structure

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Stereochemical Assessment of (φ,ψ) Outliers in Protein Structures Using Bond Geometry-Specific Ramachandran Steric-Maps.
Structure ( IF 4.4 ) Pub Date : 2019-10-10 , DOI: 10.1016/j.str.2019.09.009
Ashraya Ravikumar ₁ , Chandrasekharan Ramakrishnan ₁ , Narayanaswamy Srinivasan ₁

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Ramachandran validation of protein structures is commonly performed using developments, such as MolProbity. We suggest tailoring such analyses by position-wise, geometry-specific steric-maps, which show (φ,ψ) regions with steric-clash at every residue position. These maps are different from the classical steric-map because they are highly sensitive to bond length and angle values that are used, in our steric-maps, as observed in the residue positions in super-high-resolution peptide and protein structures. (φ,ψ) outliers observed in such structures seldom have steric-clash. Therefore, we propose that a (φ,ψ) outlier is unacceptable if it is located within the steric-clash region of a bond geometry-specific steric-map for a residue position. These steric-maps also suggest position-specific accessible (φ,ψ) space. The PARAMA web resource performs in-depth position-wise analysis of protein structures using bond geometry-specific steric-maps.

中文翻译：

使用键几何特定的Ramachandran Steric-Maps对蛋白质结构中（φ，ψ）离群值进行立体化学评估。

Ramachandran对蛋白质结构的验证通常使用诸如MolProbity这样的开发工具来进行。我们建议通过按位置排列的，特定于几何图形的空间图来裁剪此类分析，该图显示（φ，ψ）在每个残基位置处都有空间冲突的区域。这些图谱不同于经典的空间图谱，因为它们对在我们的空间图谱中使用的键长和角度值高度敏感，正如在超高分辨率肽和蛋白质结构中的残基位置所观察到的那样。在此类结构中观察到的（φ，ψ）异常值很少具有空间冲突。因此，我们提出（φ，ψ）离群值是不可接受的，如果它位于键几何特定空间图的残基位置的空间冲突区域内。这些空间图还建议特定于位置的可访问（φ，ψ）空间。

更新日期：2019-10-10

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