Estimation of protein secondary structure from circular dichroism spectra:Comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set

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-wo rkers 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 varyi ng from 29 to 48. The performance of three popular methods for estimating p rotein secondary structure fractions from CD spectra (implemented in softwa re 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 her e, and a aa-protein reference set. Secondary structure assignments from DSS P were used in the analysis. The performances of all three methods were com parable, in spite of the differences in the algorithms used in the three so ftware packages. While CDSSTR performed the best with a smaller reference s et and larger wavelength range, and CONTIN/LL performed the best with a lar ger reference set and smaller wavelength range, the performances for indivi dual secondary structures were mixed. Analyzing protein CD spectra using al l three methods should improve the reliability of predicted secondary struc tural fractions. The three programs are provided in CDPro software package and have been modified for easier use with the different reference sets des cribed in this paper. CDPro software is available at the website: http:/lam ar.colostate.edu/ similar to sreeram/CDPro. (C) 2000 Academic Press.