Estimation of protein secondary structure from synchrotron radiation circular dichroism spectra

A new approach to estimate the fraction of secondary structures fractions from synchrotron radiation circular dichroism (SRCD) spectra is presented. The protein SRCD spectra are first approximated using radial basis function networks (RBFN) and the resulting set is used to train a self-organising map (SOM). Thus the data are arranged in a two-dimensional map in such a way that most similar proteins are close to each other and vice versa. Estimation of the parallel and antiparallel beta sheets is discussed. The number of spectra in the training set is twenty four proteins and the protein under examination is also included in the set. Estimation results shows improvements compared with previous methods such as K2D and SOMCD.