Estimation of protein secondary structure from circular dichroism spectra: Comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set
Estimation of protein secondary structure from circular dichroism spectra: Comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set
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DOI：
10.1006/abio.2000.4880
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发表时间：
2000-12-15
影响因子：
2.9
通讯作者：
Woody, RW
中科院分区：
文献类型：
--
作者：
Sreerama, N;Woody, RW
我们通过纳入11种额外的蛋白质（从杨及其同事以及基德林及其同事的参考集中选取）扩展了SELCON3中使用的蛋白质参考集。根据波长范围以及参考集中是否包含变性蛋白质，构建了五个参考集，参考蛋白质的数量从29到48不等。使用此处描述的五个参考集以及一个氨基酸 - 蛋白质参考集，检验了三种从圆二色光谱估计蛋白质二级结构组分的常用方法（在CONTIN、SELCON3和CDSSTR软件包中实现）以及CONTIN的一个变体CONTIN/LL（它在CONTIN的局部线性化模型中纳入了变量选择方法）的性能。分析中使用了来自DSSP的二级结构归属。尽管三个软件包中使用的算法存在差异，但所有三种方法的性能相当。虽然CDSSTR在较小的参考集和较大的波长范围时表现最佳，CONTIN/LL在较大的参考集和较小的波长范围时表现最佳，但单个二级结构的性能则参差不齐。使用所有三种方法分析蛋白质圆二色光谱应能提高预测的二级结构组分的可靠性。这三个程序在CDPro软件包中提供，并已针对本文所述的不同参考集进行了修改以便于使用。CDPro软件可在以下网站获取：http:/lamar.colostate.edu/ 类似于sreeram/CDPro。（C）2000年学术出版社。
We have expanded the reference set of proteins used in SELCON3 by including 11 additional proteins (selected from the reference sets of Yang and co-workers and Keiderling and co-workers). Depending on the wavelength range and whether or not denatured proteins are included in the reference set, five reference sets were constructed with the number of reference proteins varying from 29 to 48. The performance of three popular methods for estimating protein secondary structure fractions from CD spectra (implemented in software packages CONTIN, SELCON3, and CDSSTR) and a variant of CONTIN, CONTIN/LL, that incorporates the variable selection method in the locally linearized model in CONTIN, were examined using the five reference sets described here, and a aa-protein reference set. Secondary structure assignments from DSSP were used in the analysis. The performances of all three methods were comparable, in spite of the differences in the algorithms used in the three software packages. While CDSSTR performed the best with a smaller reference set and larger wavelength range, and CONTIN/LL performed the best with a larger reference set and smaller wavelength range, the performances for individual secondary structures were mixed. Analyzing protein CD spectra using all three methods should improve the reliability of predicted secondary structural fractions. The three programs are provided in CDPro software package and have been modified for easier use with the different reference sets described in this paper. CDPro software is available at the website: http:/lamar.colostate.edu/ similar to sreeram/CDPro. (C) 2000 Academic Press.