Prediction of Protein Structure Classes with Ensemble Classifiers | SpringerLink
Skip to main content

Prediction of Protein Structure Classes with Ensemble Classifiers

  • Conference paper
Intelligent Computing in Bioinformatics (ICIC 2014)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 8590))

Included in the following conference series:

Abstract

Protein structure prediction is an important area of research in bioinformatics. In this research, a novel method to predict the structure of the protein is introduced. The amino acid frequencies, generalization dipeptide composition and typical hydrophobic composition of protein structure are treated as candidate feature. Flexible neural tree and neural network are employed as classification model. To evaluate the efficiency of the proposed method, a classical protein sequence dataset (1189) is selected as the test dataset. The results show that the method is efficient for protein structure prediction.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+ Basic
¥17,985 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
JPY 3498
Price includes VAT (Japan)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
JPY 5719
Price includes VAT (Japan)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
JPY 7149
Price includes VAT (Japan)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Similar content being viewed by others

References

  1. Levitt, M., Chothia, C.: Structural patterns in globular proteins. Nature 261, 552–558 (1976)

    Article  Google Scholar 

  2. Chou, K.C.: A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins 21, 319–344 (1995)

    Article  Google Scholar 

  3. Xu Y&Xu, D.: Protein threading using PROSPECT: Design and evaluation. Proteins: Structure, Function, and Genetics 40, 343–354 (2000)

    Article  Google Scholar 

  4. Chothia, C., Lesk, A.M.: The relation between the divergence of sequence and structure in proteins. EMBO J. 5, 823–826 (1986)

    Google Scholar 

  5. Chothia, C., Lesk, A.M.: The relation between the divergence of sequence and structure in proteins. EMBO J. 5(4), 823–826 (1986)

    Google Scholar 

  6. Chung, S.Y., Subbiah, S.: A structural explanation for the twilight zone of protein sequence homology. Structure 4, 1123–1127 (1996)

    Article  Google Scholar 

  7. Kaczanowski, S., Zielenkiewicz, P.: Why similar protein sequences encode similar three-dimensional structures. Theoretical Chemistry Accounts 125, 543–550 (2010)

    Article  Google Scholar 

  8. Bairoch, A., Apweiler, R., Wu, C.H., et al.: The Universal Protein Resource (UniProt). Nucleic Acids Res. 33(Database Issue), D154–D159 (2005)

    Google Scholar 

  9. Helliwell, J.R.: Protein crystal perfection and its application. Acta Crystallographica D61(pt. 6): 793–798 (2005)

    Google Scholar 

  10. Nassif, H., Al-Ali, H., Khuri, S., Keirouz, W.: Prediction of protein-glucose binding sites using support vector machines. Proteins 77(1), 121–132 (2009)

    Article  Google Scholar 

  11. Söding, J.: Protein homology detection by HMM-HMM comparison. Bioinformatics 21(7), 951–960 (2005)

    Article  Google Scholar 

  12. Wang, Y., Wu, L.Y., Zhang, X.S., Chen, L.: Automatic classification of protein structures based on convex hull representation by integrated neural network. In: Cai, J.-Y., Cooper, S.B., Li, A. (eds.) TAMC 2006. LNCS, vol. 3959, pp. 505–514. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  13. Zhang, X.S., Zhan, Z.W., Wang, Y., Wu, L.Y.: An Attempt to Explore the Similarity of Two Proteins by Their Surface Shapes. In: Operations Research and Its Applications. Lecture Notes in Operations Research, vol. 5, pp. 276–284. World Publishing Corporation, Beijing (2005)

    Google Scholar 

  14. Kohonen, J., Talikota, S., Corander, J., Auvinen, P., Arjas, E.: A Naive Bayes classifier for protein function prediction. Silico. Biol. 9(1-2), 23–34 (2009)

    Google Scholar 

  15. Wang, Z.-X., Yuan, Z.: How good is the prediction of protein structural class by the component-coupled method? Proteins 38, 165–175 (2000)

    Article  Google Scholar 

  16. Zhang, C.T., Chou, K.C.: An optimization approach to predicting protein structural class from amino-acid composition. Protein Science 1, 401–408 (1992)

    Article  Google Scholar 

  17. Zhang, C.T., Chou, K.C., Maggiora, G.M.: Predicting protein structural classes from amino acid composition: application of fuzzy clustering. Protein Engineering 8, 425–435 (1995)

    Article  Google Scholar 

  18. Kedarisetti, K., Kurgan, L., Dick, S.: A comment on Prediction of protein structural classes by a new measure of information discrepancy (2006) (accepted)

    Google Scholar 

  19. Kedarisetti, K.D., Kurgan, L., Dick, S.: Classifier ensembles for protein structural class prediction with varying homology. Biochemical and Biophysical Research Communications 348, 981–988 (2006)

    Article  Google Scholar 

  20. Liu, T., Jia, C.: A high-accuracy protein structural class prediction algorithm using predicted secondary structural information. J. Theor. Biol. 267, 272–275 (2010)

    Article  Google Scholar 

  21. Shao, G., Chen, Y.: Predict the Tertiary Structure of Protein with Flexible Neural Tree. In: Huang, D.-S., Ma, J., Jo, K.-H., Gromiha, M.M. (eds.) ICIC 2012. LNCS, vol. 7390, pp. 324–331. Springer, Heidelberg (2012)

    Chapter  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer International Publishing Switzerland

About this paper

Cite this paper

Bao, W., Chen, Y., Wang, D., kong, F., Yu, G. (2014). Prediction of Protein Structure Classes with Ensemble Classifiers. In: Huang, DS., Han, K., Gromiha, M. (eds) Intelligent Computing in Bioinformatics. ICIC 2014. Lecture Notes in Computer Science(), vol 8590. Springer, Cham. https://doi.org/10.1007/978-3-319-09330-7_40

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-09330-7_40

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-09329-1

  • Online ISBN: 978-3-319-09330-7

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics