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TertProt: A Protein Fold Recognition Method Using Protein Secondary Structure Program

  • D. S. V. G. K. Kaladhar
Conference paper
Part of the Advances in Intelligent and Soft Computing book series (AINSC, volume 132)

Abstract

TertProt is a protein secondary structure program written in ANSI C language implemented using Chou-Fasman conformational parameters with tertiary structure prediction methodology. The secondary structure is a key element for the analysis and modelling of protein structure. The TertProt method for modeling of a 3D structure of a protein is done using Colloc’h triangle has been designed in the present research. The structures has been compared with Oxytocin, HCMV protease, D, L altering peptide and Alzhemer beta amyloid peptides.

Keywords

Chou-Fasman Colloc’h triangle C program 

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References

  1. 1.
    Wolfgang, K., Christian, S.: Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577–2637 (1983)CrossRefGoogle Scholar
  2. 2.
    Dmitrij, F., Patrick, A.: Knowledge-Based Protein Secondary Structure Assignment. Proteins: Structure, Function, and Genetics 23, 566–579 (1995)CrossRefGoogle Scholar
  3. 3.
    Floudas, C.A., Fung, H.K., McAllister, S.R., Mönnigmann, M., Rajgaria, R.: Advances in protein structure prediction and de novo protein design: A review. Chemical Engineering Science 61, 966–988 (2006)CrossRefGoogle Scholar
  4. 4.
    Andrea, D.W., Leroy, H.: Systems Biology, Proteomics, and the Future of Health Care: Toward Predictive, Preventative, and Personalized Medicine. Journal of Proteome Research 3, 179–196 (2004)CrossRefGoogle Scholar
  5. 5.
    Friedberg, E.C.: Biological Responses to DNA Damage: A Perspective in the New Millennium. Quant. Biol. 65, 593–602 (2000)Google Scholar
  6. 6.
    Howard, J.F., Christopher, W.V.H.: A fast method to sample real protein conformational space. Proteins: Structure, Function, and Bioinformatics 39, 112–131 (2000)CrossRefGoogle Scholar
  7. 7.
    David, T.J.: A Practical Guide to Protein Structure Prediction. Methods in Molecular Biology 143, 131–154 (2000)Google Scholar
  8. 8.
    Tina, A.E., Linda, P., Janet, M.T.: Computational analysis of α-helical membrane protein structure: implications for the prediction of 3D structural models. Protein Engineering, Design and Selection 17, 613–624 (2004)CrossRefGoogle Scholar
  9. 9.
    Fabrizio, C., Niccolò, T., Paul, M.W., Monica, B., Francesca, M., Massimo, S., Christopher, M.D.: Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding. Nature Structural Biology 6, 1005–1009 (1999)CrossRefGoogle Scholar
  10. 10.
    Cooke, P.: The molecular biology revolution and the rise of bioscience megacentres in North America and Europe. Environment and Planning C: Government and Policy 22, 161–177 (2004)CrossRefGoogle Scholar
  11. 11.
    Chen, Y., Blackwell, T.W., Chen, J., Gao, J., Lee, A.W., et al.: Integration of Genome and Chromatin Structure with Gene Expression Profiles To Predict c-MYC Recognition Site Binding and Function. PLoS Comput. Biol. 3, e63 (2007)Google Scholar
  12. 12.
    Michael, L.C.: The molecular surface package. Journal of Molecular Graphics 11, 139–141 (1993)CrossRefGoogle Scholar
  13. 13.
    Anne, B.C., Julie, N., Laurent, B., Serge, H.: “Iso-depth contour map” of a molecular surface. of a molecular surface. Journal of Molecular Graphics 12, 162–168 (1994)Google Scholar
  14. 14.
    Franck, D., Jean-François, S., Jean-Paul, M.: Protein secondary structure assignment through Voronoï tessellation. Proteins: Structure, Function, and Bioinformatics 55, 519–528 (2004)CrossRefGoogle Scholar
  15. 15.
    Colloc’h, N., Etchebest, C., Thoreau, E., Henrissat, B., Mornon, J.P.: Comparison of three algorithms for the assignment of secondary structure in proteins: the advantages of a consensus assignment. Protein Eng. 6, 377–382 (1993)CrossRefGoogle Scholar
  16. 16.
    Rajbir, S., Sumandeep, K.D., Parvinder, S.S.: Chou-Fasman Method for Protein Structure Prediction using Cluster Analysis. World Academy of Science, Engineering and Technology 72, 982–987 (2010)Google Scholar
  17. 17.
    Labesse, G., Colloc’h, N., Pothier, J., Mornon, J.R.: P-SEA: a new efficient assignment of secondary structure from C trace of proteins. CABIOS 13, 291–295 (1997)Google Scholar
  18. 18.
    Joachim, S., Theo, M., Thomas, L.: Decicion tree-based formation of consensus protein secondary structure prediction. Bioinformatics 15, 1039–1046 (1999)CrossRefGoogle Scholar
  19. 19.
    Brickman, J., Heiden, W., Vollhardt, H., Zachmann, C.D.: New man-machine communication strategies in molecular modeling. In: Hawaii International Conference on System Sciences (HICSS 1995), p. 273 (1995)Google Scholar
  20. 20.
    Dmitri, I.S., Maxim, V.P., Michel, H.J.K.: Determination of Domain Structure of Proteins from X-Ray Solution Scattering. Biophysical Journal 80, 2946–2953 (2001)CrossRefGoogle Scholar
  21. 21.
    Nicolas, G., Manuel, C.P.: SWISS-MODEL and the Swiss-Pdb Viewer: An environment for comparative protein modeling. Electrophoresis 18, 2714–2723 (1997)CrossRefGoogle Scholar
  22. 22.
    Amos, B., Rolf, A.: The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucl. Acids Res. 26, 38–42 (1998)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • D. S. V. G. K. Kaladhar
    • 1
  1. 1.Department of BioinformaticsGIS, GITAM UniversityVisakhapatnamIndia

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