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Identification of Protein Interaction Partners from Shape Complementarity Molecular Cross-Docking

  • Elodie Laine
  • Alessandra Carbone
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8158)

Abstract

There is a growing interest in using efficient shape complementarity docking algorithms to analyze protein-protein interactions at a large scale. We have realized complete cross-docking of several tens of enzyme/inhibitors proteins. On the one hand, we demonstrate that docking score distributions for the known complexes are not distinguishable from those for the non-interacting pairs. On the other hand, we show that the knowledge of the experimental interfaces applied to the docking conformations permits to retrieve true interaction partners with high accuracy. We further identify the determinants of the molecular recognition between true interactors compared to non-interacting proteins.

Keywords

Protein Pair Docking Score Interaction Index Docking Algorithm Conformational Ensemble 
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.

References

  1. 1.
    Andreani, J., Faure, G., Guerois, R.: Versatility and invariance in the evolution of homologous heteromeric interfaces. PLoS Comput. Biol. 8, e1002677 (2012)CrossRefGoogle Scholar
  2. 2.
    Gray, J.J.: High-resolution protein-protein docking. Curr. Opin. Struct. Biol. 16, 183–193 (2006)CrossRefGoogle Scholar
  3. 3.
    Hubbard, S., Thornton, J.: NACCESS. Tech. rep., Computer Program, Dept of Biochemistry and Molecular Biology, University College London (1993)Google Scholar
  4. 4.
    Janin, J.: Protein-protein docking tested in blind predictions: the CAPRI experiment. Mol. Biosyst. 6, 2351–2362 (2010)CrossRefGoogle Scholar
  5. 5.
    Levy, E.D.: A simple definition of structural regions in proteins and its use in analyzing interface evolution. J. Mol. Biol. 403, 660–670 (2010)CrossRefGoogle Scholar
  6. 6.
    Lopes, A., Sacquin-Mora, S., Dimitrova, V., Laine, E., Ponty, Y.: Protein-protein interactions in a crowded environment via cross-docking and evolutionary information (submitted, 2013)Google Scholar
  7. 7.
    Mintseris, J., Wiehe, K., Pierce, B., Anderson, R., Chen, R., Janin, J., Weng, Z.: Protein-Protein Docking Benchmark 2.0: An update. Proteins 60, 214–216 (2005)CrossRefGoogle Scholar
  8. 8.
    Ritchie, D.W., Kemp, G.J.: Protein docking using spherical polar Fourier correlations. Proteins 39, 178–194 (2000)CrossRefGoogle Scholar
  9. 9.
    Sacquin-Mora, S., Carbone, A., Lavery, R.: Identification of protein interaction partners and protein-protein interaction sites. J. Mol. Biol. 382, 1276–1289 (2008)CrossRefGoogle Scholar
  10. 10.
    Wass, M.N., Fuentes, G., Pons, C., Pazos, F., Valencia, A.: Towards the prediction of protein interaction partners using physical docking. Mol. Syst. Biol. 7, 469 (2011)CrossRefGoogle Scholar
  11. 11.
    Wilcoxon, F.: Individual comparisons by ranking methods. Biometrics Bull. 1, 80–83 (1945)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Elodie Laine
    • 1
    • 2
  • Alessandra Carbone
    • 1
    • 2
  1. 1.UMR 7238, Equipe de Génomique AnalytiqueUniversité Pierre et Marie CurieParisFrance
  2. 2.CNRS, UMR 7238, Laboratoire de Génomique des MicroorganismesUniversité Pierre et Marie CurieParisFrance

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