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Identifying Protein-Protein Interaction Sites Using Granularity Computing of Quotient Space Theory

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Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 6401))

Abstract

The function of protein-protein interaction is very important to cell activity. Studying protein-protein interaction can help us understand life activities and pharmaceutical design. In this study, a kernel covering algorithm combined with the theory of granular computing of quotient space for predicting protein-protein interaction sites is proposed, (i.e. KCA-GS Model). This method achieves good performances, and the Sensitivity, Specificity, Accuracy and Correlation coefficient are 52.97%, 53.92%, 70.27%, 24.61%, respectively. It is indicated that our method is effective, potential and promising to identify protein-protein interaction sites.

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References

  1. Mitchell, D.A., Marshall, T.K., Deschenes, R.J.: Vectors for the inducible overexpression of glutathione S-transferase fusion proteins in yeast. Yeast 9(7), 715–722 (1993)

    Article  Google Scholar 

  2. Harlow, E., Whyte, P., Franza, B.R., et al.: Association of adenovirus early-region 1A proteins with cellular polypeptides. MolCellBiol. 6(5), 157–1589 (1986)

    Google Scholar 

  3. Mrowka, R., Patzak, A., Herzel, H.: Is there a bias in proteome research?, vol. 11, pp. 1971–1973. Cold Spring Harbor Laboratory Press, New York (2001)

    Google Scholar 

  4. Huang, X.Z., Shan, Y.B.: Prediction of Protein Interaction Sites From Sequence Profile and Residue Neighbor List. Proteins: Structure, Function, and Genetics 44, 336–343 (2001)

    Article  Google Scholar 

  5. James, R., Bradford, D.R.: Westhead. Improved Prediction of Protein-protein Binding Sites Using a Support Vector Machines Approach. Bioinformatics 21(8), 1487–1494 (2005)

    Google Scholar 

  6. Wang, B., San Wong, H., Huang, D.S.: Inferring protein-protein interacting sites using residue conservation and evolutionary information. Protein Pept. Lett. 13, 999–1005 (2006)

    Article  Google Scholar 

  7. Zhu, H., Domingues, F.S., Sommer, I., Lengauer, T.: NOXclass: prediction of protein-protein interaction types. BMC Bioinformatics 7, 27 (2006)

    Article  Google Scholar 

  8. Zhang, L., Zhang, B.: A geometrical representation of McCulloch-Pitts neural model andits applications. IEEE Trans. Neural Netw. 10, 925–929 (1999)

    Article  Google Scholar 

  9. Zhang, L., Zhang, B., Yin, H.F.: An alternative covering design algorithm of multi-layer neural networks. J. Soft. 10, 737–742 (1999)

    Google Scholar 

  10. Zhang, B., Zhang, L.: Theory and Applications of problem solving. Tsinghua University Press, Beijing (1990)

    Google Scholar 

  11. Zhang, L., Zhang, B.: The quotient space theory of problem solving. In: Wang, G., Liu, Q., Yao, Y., Skowron, A. (eds.) RSFDGrC 2003. LNCS (LNAI), vol. 2639, pp. 11–15. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  12. Fariselli, P., Pazos, F., Valencia, A., et al.: Prediction of protein-protien interaction sites in heterocompleses with neural networks. Eur. J. Bichem. 269(5), 1356–1361 (2002)

    Article  Google Scholar 

  13. Altschul, S.F., Madden, T.L., Schaffer, A.A., et al.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17), 3389–3402 (1997)

    Article  Google Scholar 

  14. Rost, B., Sander, C.: Conservation and prediction of solvent accessibility in protein families. Proteins 20, 216–226 (1994)

    Article  Google Scholar 

  15. Young, L., Jernigan, R.L., Covell, D.G.: A role for surface hydrophobicity in protein-protein recognition. Protein Sci. 3, 717–729 (1994)

    Article  Google Scholar 

  16. Young, L., Jernigan, R.L., Covell, D.G.: A role for surface hydrophobicity in protein-protein recognition. Protein Sci. 3, 717–729 (1994)

    Article  Google Scholar 

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Zhang, Y., Wang, Y., Ma, J., Chen, X. (2010). Identifying Protein-Protein Interaction Sites Using Granularity Computing of Quotient Space Theory. In: Yu, J., Greco, S., Lingras, P., Wang, G., Skowron, A. (eds) Rough Set and Knowledge Technology. RSKT 2010. Lecture Notes in Computer Science(), vol 6401. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16248-0_103

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  • DOI: https://doi.org/10.1007/978-3-642-16248-0_103

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-16247-3

  • Online ISBN: 978-3-642-16248-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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