Protein Secondary Structure Class Assignment on the Basis of a New Graphic Representation

A novel 2D representation (M-curve) has been provided to visualize the structure information of protein secondary structure sequences: (1) end point of the curve reflects difference of amino acid residue numbers in alpha-helices and beta-strands of a protein; (2) Up/down ladder-like structures in the curve show that alpha-helices/beta-strands appear sequentially in this region; (3) triangular-like/trapeziform-like structures of the curve show that alpha-helices and beta-strands appear alternatively in this region. So from the M-curve, a protein could be directly assigned into corresponding secondary structure class. Moreover, a new numerical descriptor, four-component vector, is introduced and applied to cluster analysis. (C) 2008 Wiley Periodicals, Inc. Int J Quantum Chem 109: 819-825, 2009