K2D2: Estimation of protein secondary structure from circular dichroism spectra

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.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.Circular dichroism (CD) spectroscopy is a widely used technique to analyze the secondary structure of proteins in solution. It is based on the dependence of the optical activity of the protein in the 170–240 nm wavelength with the backbone orientation of the peptide bonds with minor influences from the side chains [1]. Different types of secondary structure producing characteristic spectra, the spectrum of a given protein can be used to estimate its percentage content on the major secondary structure types. During the past 30 years, many methods that address this problem have been developed, which apply a variety of approaches from singular value decomposition to optimization algorithms, regression or neural networks [2-13]. One of these methods is K2D [8]. It uses a self-organizing map (SOM) algorithm, a type of neural network. Spectra from proteins with solved tertiary structure are used as training set to produce the SOM. From the resulting map of spectra, "secondary structure maps" are derived. The secondary structure map is directly related to the spectra 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.Here we present K2D2, a re-implementation of K2D using the latest version of the SOM_PAK package [14]. K2D2 accepts a broader wavelength range for the input spectra, 190 to 240 nm further to the 200