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

BMB Reports

Volumn 44, Issue 2, 2011, Pages 118-122

  Park, Sang Youn ^a   Yoo, Min Jae ^a   Shin, Jaemin ^b   Cho, Kwang Hwi ^a  

^a Soongsil University   (South Korea)

^b SBScience Inc   (South Korea)

Author keywords

helix; strand; 310 helix; Pseudo center; Secondary structure identification

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; CHEMISTRY; COMPUTER PROGRAM; PROTEIN DATABASE; PROTEIN SECONDARY STRUCTURE;

ALGORITHMS; DATABASES, PROTEIN; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SOFTWARE;

EID: 79952049726     PISSN: 19766696     EISSN: 1976670X     Source Type: Journal    
DOI: 10.5483/BMBRep.2011.44.2.118     Document Type: Article

References (15)

1. Pauling, L., Corey, R. B. and Branson, H. R. (1951) The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain. Proc. Natl. Acad. Sci. U.S.A. 37, 205-211.
2. Pauling, L. and Corey, R. B. (1951) The pleated sheet, a new layer configuration of polypeptide chains. Proc. Natl. Acad. Sci. U.S.A. 37, 251-256.
3. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. and Bourne, P. E. (2000) The Protein Data Bank. Nucleic Acids Res. 28, 235-242.
4. Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637.
5. Frishman, D. and Argos, P. (1995) Knowledge-based protein secondary structure assignment. Proteins 23, 566-579.
6. Richards, F. M. and Kundrot, C. E. (1988) Identification of structural motifs from protein coordinate data: secondary structure and first-level supersecondary structure. Proteins 3, 71-74.
7. Labesse, G., Colloc'h, N., Pothier, J. and Mornon, J. P. (1997) P-SEA: a new efficient assignment of secondary structure from Cα trace of proteins. Comput. Appl. Biosci. 13, 291-295.
8. Martin, J., Letellier, G., Martin, A., Taly, J. F., Brevern, A. G. D. and Gibrat, G. F. (2005) Protein secondary structure assignment revisited: a detailed analysis of different assignment methods. BMC Struct Biol. 5, 17.
9. Sklenar, H., Etchebest, C. and Lavery R. (1989) Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis. Proteins 6, 46-60.
10. King, S. M. and Johnson, W. C. (1999) Assigning secondary structure from protein coordinate data. Proteins 3, 313-320.
11. Fodje, M. N. and Al-Karadaghi, S. (2002) Occurrence, conformational features and amino acid propensities for the π-helix. Protein Eng. 15, 353-358.
12. Cubellis, M. V., Cailliez, F. and Lovell, S. C. (2005) Secondary structure assignment that accurately reflects physical and evolutionary characteristics. BMC Bioin-formatics. 6, S8.
13. Dupuis, F., Sadoc, J. F. and Mornon, J. P. (2004) Protein secondary structure assignment through voronoi tessellation. Proteins 55, 519-528.
14. Colloc'h, N., Etchebest, C., Thoreau, E., Henrissat, B. and Mornon, J. P. (1993) Comparison of three algorithms for the assignment of secondary structure in proteins: the advantages of a consensus assignment. Protein Eng. 6, 377-382.
15. Zhang, W., Dunker, A. K. and Zhou, Y. (2008) Assessing secondary structure assignment of protein structures by using sequence-alignment benchmarks. Proteins 71, 61-67.