title: 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 Cα information have been under development as well, but their accuracy is only ~80% compared to DSSP. We have hereby developed SABA (Secondary Structure Assignment Program Based on only Alpha Carbons) with~90% accuracy. SABA defines a novel geometrical parameter, termed a pseudo center, which is the midpoint of two continuous Cαs. SABA is capable of identifying α-helices, 3(10)-helices, and β-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 Cα-only structures, algorithms using limited Cα information with high accuracy have the potential to enhance the speed of calculations for high capacity structure comparison.
authors.affiliation: School of Systems Biomedical Science, Soongsil University, Seoul 156-743, Korea.
authors.forename: Sang Youn
authors.initials: SY
authors.lastname: Park
authors.forename: Min-Jae
authors.initials: MJ
authors.lastname: Yoo
authors.forename: Jaemin
authors.initials: J
authors.lastname: Shin
authors.forename: Kwang-Hwi
authors.initials: KH
authors.lastname: Cho
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry; D012984:Software
chemical_list: D011506:Proteins