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Protein Contact Prediction by Integrating Joint Evolutionary Coupling Analysis and Supervised Learning

  • Jianzhu Ma
  • Sheng Wang
  • Zhiyong Wang
  • Jinbo Xu
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9029)

Abstract

Residue-residue contacts play an important role in maintaining the native fold of a protein and guiding protein folding. However, contact prediction from sequence is very challenging, as indicated by CASP10 [1], which shows that long-range contact prediction accuracy on hard targets is only ~20%.

Keywords

Random Forest Supervise Learning Method Pfam Family Gaussian Graphical Model Contact Prediction 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    Monastyrskyy, B., D’Andrea, D., Fidelis, K., Tramontano, A., Kryshtafovych, A.: Evaluation of residue-residue contact prediction in CASP10. Proteins 82(Suppl. 2), 138–153 (2014)CrossRefGoogle Scholar
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    Jones, D.T., et al.: PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics 28(2), 184–190 (2012)CrossRefGoogle Scholar
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    Do, C.B., Gross, S.S., Batzoglou, S.: CONTRAlign: discriminative training for protein sequence alignment. In: Apostolico, A., Guerra, C., Istrail, S., Pevzner, P.A., Waterman, M. (eds.) RECOMB 2006. LNCS (LNBI), vol. 3909, pp. 160–174. Springer, Heidelberg (2006)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Jianzhu Ma
    • 1
  • Sheng Wang
    • 1
  • Zhiyong Wang
    • 1
  • Jinbo Xu
    • 1
  1. 1.Toyota Technological Institute at ChicagoChicagoUSA

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