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

• Published in: BMB reports Vol. 44; no. 2; pp. 118 - 122
• Main Authors: Park, S.Y., Soongsil University, Seoul, Republic of Korea, Yoo, M.J., Soongsil University, Seoul, Republic of Korea, Shin, J.M., SBScience, Inc., Sungnam, Republic of Korea, Cho, K.H., Soongsil University, Seoul, Republic of Korea
• Format: Journal Article
• Language: English
• Published: Korea (South) 생화학분자생물학회 01.02.2011
• Subjects: Algorithms; alpha-helix; beta-strand; Databases, Protein; HELIX; Protein Structure, Secondary; Proteins - chemistry; Pseudo center; Secondary structure identification; Software; 화학
• ISSN: 1976-6696; 1976-670X
• DOI: 10.5483/BMBRep.2011.44.2.118

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.