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K2D2: Estimation of protein secondary structure from circular dichroism spectra

Carolina Perez-Iratxeta1* and Miguel A Andrade-Navarro123

Author Affiliations

1 Ontario Genomics Innovation Centre, Ottawa Health Research Institute, 501 Smyth, Ottawa, ON, K1H 8L6, Canada

2 Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Canada

3 Computational Biology and Data Mining Group, Max Delbrück Centre for Molecular Medicine, Berlin, Germany

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BMC Structural Biology 2008, 8:25  doi:10.1186/1472-6807-8-25

Published: 13 May 2008

Abstract

Background

Circular dichroism spectroscopy is a widely used technique to analyze the secondary structure of proteins in solution. Predictive methods use the circular dichroism spectra from proteins of known tertiary structure to assess the secondary structure contents of a protein with unknown structure given its circular dichroism spectrum.

Results

We developed K2D2, a method with an associated web server to estimate protein secondary structure from circular dichroism spectra. The method uses a self-organized map of spectra from proteins with known structure to deduce a map of protein secondary structure that is used to do the predictions.

Conclusion

The K2D2 server is publicly accessible at http://www.ogic.ca/projects/k2d2/ webcite. It accepts as input a circular dichroism spectrum and outputs the estimated secondary structure content (alpha-helix and beta-strand) of the corresponding protein, as well as an estimated measure of error.