Secondary structure assignment for conformationally irregular peptides: Comparison between DSSP, STRIDE and KAKSI
Secondary structure (SS) assignment codes converge well in regular proteins. Intrinsically disordered and unfolded proteins have residual or transient SS, difficult to characterize experimentally. We characterized the SS overlap for several disordered peptides, and find overlap as low as 49%. Main differences are observed in turns, distinction between alpha and 310 helices, and short parallel sheets.
residual transient secondary structure intrinsically disordered proteins gp41 asparagine