Secondary structure determination of proteins in aqueous solution by infrared spectroscopy: A comparison of multivariate data analysis methods
Secondary structure determination of proteins in aqueous solution by infrared spectroscopy: A comparison of multivariate data analysis methods
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DOI：
10.1006/abio.1996.0369
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发表时间：
1996-10-01
影响因子：
2.9
通讯作者：
Hubner, W
中科院分区：
文献类型：
--
作者：
Rahmelow, K;Hubner, W
利用不同的多元数据分析方法，对已知x射线结构的39种蛋白质红外光谱数据库中二级结构预测的准确性进行了研究。如果同时使用酰胺I和酰胺II波段进行校准，则与x射线晶体学测定的二级结构最吻合。通过优化参数，奇异值分解、偏最小二乘和脊回归方法得到了相似的结果。从预测的标准误差判断，二级结构单元helix和beta-sheet的预测精度最高。小于20个蛋白质光谱的小数据集二级结构含量存在差异，采用柱交叉验证可以提高预测精度；然而，使用这些校准集，所有39种蛋白质的平均二级结构预测都降低了。与指定的二级结构类型螺旋和β -片相比，预测氢键弯或桥具有更高的精度。(C) 1996学术出版社，Inc.
The accuracy of the secondary structure prediction from an infrared spectra data base of 39 proteins with known X-ray structure was investigated by different methods of multivariate data analysis. The best agreements with the secondary structure determined by X-ray crystallography are obtained if both the amide I and amide II bands are used for calibration. With optimized parameters the methods singular value decomposition, partial least squares, and ridge regression yield similar results. As judged by the standard error of prediction, the secondary structure elements helix and beta-sheet can be predicted with the highest accuracy. Small data sets of less than 20 protein spectra, which exhibit the variance in secondary structure content of the whole set, can pretend an increased prediction accuracy only if column cross-validation is used as reference; however, with these calibration sets the average secondary structure prediction of all 39 proteins is debased. The hydrogen-bonded turns or bridges are predicted with higher accuracy than the assigned secondary structure types helix and beta-sheet. (C) 1996 Academic Press, Inc.