Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
Structure. 2019 Dec 3;27(12):1875-1884.e2. doi: 10.1016/j.str.2019.09.009. Epub 2019 Oct 10.
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.
Ramachandran 结构验证通常使用 MolProbity 等方法进行。我们建议通过位置特异性、几何特异性的空间位阻图来定制这些分析，这些位阻图显示了每个残基位置的（φ，ψ）区域的空间位阻冲突。这些图谱与经典的空间位阻图不同，因为它们对使用的键长和角度值非常敏感，在我们的空间位阻图中，这些值是在超高分辨率肽和蛋白质结构中的残基位置观察到的。在这些结构中观察到的（φ，ψ）异常值很少有空间位阻冲突。因此，如果（φ，ψ）异常值位于残基位置的特定键几何空间位阻图的空间位阻冲突区域内，我们建议该异常值是不可接受的。这些空间位阻图还提示了特定位置的可及（φ，ψ）空间。PARAMA 网络资源使用特定键几何空间位阻图对蛋白质结构进行深入的位置分析。
