SABA (secondary structure assignment program based on only alpha carbons): a novel pseudo center geometrical criterion for accurate assignment of protein secondary structures

Abstract

Most widely used secondary structure assignment methods such as DSSP identify structural elements based on N-H and C=O hydrogen bonding patterns from X-ray or NMR-determined coordinates. Secondary structure assignment algorithms using limited C alpha information have been under development as well, but their accuracy is only similar to 80% compared to DSSP. We have hereby developed SABA (Secondary Structure Assignment Program Based on only Alpha Carbons) with similar to 90% accuracy. SABA defines a novel geometrical parameter, termed a pseudo center, which is the midpoint of two continuous C alpha s. SABA is capable of identifying alpha-helices, 3(10)-helices, and beta-strands with high accuracy by using cut-off criteria on distances and dihedral angles between two or more pseudo centers. In addition to assigning secondary structures to C alpha-only structures, algorithms using limited C alpha information with high accuracy have the potential to enhance the speed of calculations for high capacity structure comparison. [BMB reports 2011; 44(2): 118-122]