Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC 27599-7260, USA.
Bioinformatics. 2011 Aug 15;27(16):2209-15. doi: 10.1093/bioinformatics/btr374. Epub 2011 Jun 23.
Increasing use of structural modeling for understanding structure-function relationships in proteins has led to the need to ensure that the protein models being used are of acceptable quality. Quality of a given protein structure can be assessed by comparing various intrinsic structural properties of the protein to those observed in high-resolution protein structures.
In this study, we present tools to compare a given structure to high-resolution crystal structures. We assess packing by calculating the total void volume, the percentage of unsatisfied hydrogen bonds, the number of steric clashes and the scaling of the accessible surface area. We assess covalent geometry by determining bond lengths, angles, dihedrals and rotamers. The statistical parameters for the above measures, obtained from high-resolution crystal structures enable us to provide a quality-score that points to specific areas where a given protein structural model needs improvement.
We provide these tools that appraise protein structures in the form of a web server Gaia (http://chiron.dokhlab.org). Gaia evaluates the packing and covalent geometry of a given protein structure and provides quantitative comparison of the given structure to high-resolution crystal structures.
Supplementary data are available at Bioinformatics online.
越来越多地使用结构建模来理解蛋白质的结构-功能关系，这导致需要确保所使用的蛋白质模型具有可接受的质量。可以通过将蛋白质的各种固有结构特性与高分辨率蛋白质结构中观察到的特性进行比较，来评估给定蛋白质结构的质量。
在这项研究中，我们提出了用于将给定结构与高分辨率晶体结构进行比较的工具。我们通过计算总空隙体积、未满足氢键的百分比、立体冲突的数量以及可及表面积的缩放来评估包装。我们通过确定键长、角度、二面角和构象异构体来评估共价几何形状。上述测量的统计参数，是从高分辨率晶体结构中获得的，使我们能够提供一个质量分数，指出给定蛋白质结构模型需要改进的具体领域。
我们以 Gaia（http://chiron.dokhlab.org）的形式提供评估蛋白质结构的这些工具。Gaia 评估给定蛋白质结构的包装和共价几何形状，并提供给定结构与高分辨率晶体结构的定量比较。
补充数据可在 Bioinformatics 在线获得。
