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KMID : 0624620110440020118
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BMB Reports
2011 Volume.44 No. 2 p.118 ~ p.122
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SABA (secondary structure assignment program based on only alpha carbons): a novel pseudo center geometrical criterion for accurate assignment of protein secondary structures
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Park Sang-Youn
Yoo Min-Jae
Shin Jae-Min
Cho Kwang-Hwi
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Abstract
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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.
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KEYWORD
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α-helix, β-strand, Pseudo center, Secondary structure identification, 310-helix
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