Abstract
BackgroundCircular 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.ResultsWe 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.ConclusionThe K2D2 server is publicly accessible at . 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.
Highlights
Circular dichroism (CD) spectroscopy is a widely used technique to analyze the secondary structure of proteins in solution
The secondary structure map is directly related to the spectra selforganizing map (SOM) and this relation is applied to estimate the percentages of content in alpha helix and beta strand of a protein given its CD spectrum
The performance of K2D2 was measured in a left-one-out benchmark, comparing real and predicted values, by means of the Pearson correlation coefficient (r) and the
Summary
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
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