PDB2CD: a web-based application for the generation of circular dichroism spectra from protein atomic coordinates.
PDB2CD: a web-based application for the generation of circular dichroism spectra from protein atomic coordinates.
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DOI：
10.1093/bioinformatics/btw554
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发表时间：
2017-01-01
期刊：
影响因子：
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通讯作者：
Janes RW
中科院分区：
文献类型：
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作者：
Mavridis L;Janes RW
圆二色性（CD）光谱被广泛用于测定蛋白质中存在的二级结构含量的百分比。然而，尽管二级结构是一个很大的贡献者，但它并不是影响CD光谱形状和大小的唯一因素。其他结构特征也可以做出贡献，因此整个蛋白质结构构象可以产生CD光谱。需要能够从原子坐标生成蛋白质CD光谱的应用。然而，目前还没有经验得出的方法来做到这一点。PDB 2CD已被创建为从原子坐标生成蛋白质CD光谱的基于化学的方法。该方法利用蛋白质构象内的结构特征的组合;不仅其二级结构含量百分比，而且这些结构组分相对于彼此的并置，以及查询蛋白质与我们的数据集中的蛋白质的整体结构相似性，SP175数据集，从蛋白质圆二色性数据库（PCDDB）获得的“金标准”集。大量的CD光谱与71个蛋白质在这个数据集中已经产生了极好的精度，使用留一交叉验证过程。该方法还创建了与来自PCDDB的14种蛋白质的测试集的光谱非常一致的光谱。PDB 2CD软件包提供了一种基于Web的用户友好方法，使研究人员能够从蛋白质原子坐标生成CD光谱。 http://pdb2cd.cryst.bbk.ac.uk 补充数据可在Bioinformatics在线获得。
Circular dichroism (CD) spectroscopy is extensively utilized for determining the percentages of secondary structure content present in proteins. However, although a large contributor, secondary structure is not the only factor that influences the shape and magnitude of the CD spectrum produced. Other structural features can make contributions so an entire protein structural conformation can give rise to a CD spectrum. There is a need for an application capable of generating protein CD spectra from atomic coordinates. However, no empirically derived method to do this currently exists. PDB2CD has been created as an empirical-based approach to the generation of protein CD spectra from atomic coordinates. The method utilizes a combination of structural features within the conformation of a protein; not only its percentage secondary structure content, but also the juxtaposition of these structural components relative to one another, and the overall structure similarity of the query protein to proteins in our dataset, the SP175 dataset, the ‘gold standard’ set obtained from the Protein Circular Dichroism Data Bank (PCDDB). A significant number of the CD spectra associated with the 71 proteins in this dataset have been produced with excellent accuracy using a leave-one-out cross-validation process. The method also creates spectra in good agreement with those of a test set of 14 proteins from the PCDDB. The PDB2CD package provides a web-based, user friendly approach to enable researchers to produce CD spectra from protein atomic coordinates. http://pdb2cd.cryst.bbk.ac.uk Supplementary data are available at Bioinformatics online.