Advertisement

Consistent Visualization of Multiple Rigid Domain Decompositions of Proteins

  • Emily Flynn
  • Ileana StreinuEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9683)

Abstract

We describe an efficient method to facilitate the visual comparison of cluster decompositions obtained from multiple variations of a protein structure, as well as the results of using different computational and experimental methods for obtaining such decompositions. Implemented as a web server application, this tool is useful for gaining information about protein folding cores, the effect of mutations on a protein’s stability, and for validation and better understanding of rigidity analysis.

Keywords

Stable Match Parent Cluster Multiple Conformation Cluster Decomposition Consistent Coloring 
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.
    Bowers, J.C., John, R.T., Streinu, I.: Managing reproducible computational experiments with curated proteins in KINARI-2. In: Harrison, R., Li, Y., Măndoiu, I. (eds.) Bioinformatics Research and Applications. LNCS, vol. 9096, pp. 72–83. Springer, Heidelberg (2015)Google Scholar
  2. 2.
    Flynn, E., Jagodzinski, F., Santana, S.P., Streinu, I.: Rigidity and flexibility of protein-nucleic acid complexes. In: Proceedings of 3nd IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2013), June 2013Google Scholar
  3. 3.
    Fox, N., Jagodzinski, F., Li, Y., Streinu, I.: KINARI-Web: a server for protein rigidity analysis. Nucleic Acids Res. 39(Web Server Issue), W177–W183 (2011)CrossRefGoogle Scholar
  4. 4.
    Heal, J., Jimenez-Roldan, J., Wells, S., Freedman, R., Römer, R.: Inhibition of HIV-1 protease: the rigidity perspective. Bioinformatics 28, 350–357 (2012)CrossRefGoogle Scholar
  5. 5.
    Henzler-Wildmand, K., Kern, D.: Dynamic personalities of proteins. Nature 50, 964–972 (2007)CrossRefGoogle Scholar
  6. 6.
    Jagodzinski, F., Clark, P., Liu, T., Grant, J., Monastra, S., Streinu, I.: Rigidity analysis of periodic crystal structures and protein biological assemblies. BMC Bioinform. 14(Suppl. 18), S2 (2013)CrossRefGoogle Scholar
  7. 7.
    Jagodzinski, F., Hardy, J., Streinu, I.: Using rigidity analysis to probe mutation-induced structural changes in proteins. J. Bioinform. Comput. Biol. 10(3), 1242010 (2012)CrossRefGoogle Scholar
  8. 8.
    Klepeis, J.L., Lindorff-Larsen, K., Dror, R.O., Shaw, D.E.: Long-timescale molecular dynamics simulations of protein structure and function. Curr. Opin. Struct. Biol. 19(2), 120–127 (2009)CrossRefGoogle Scholar
  9. 9.
    Meuwly, M., Cui, Q.: Protein functional dynamics: from femtoseconds to milliseconds. Chem. Phys. 396, 1–2 (2012)CrossRefGoogle Scholar
  10. 10.
    Rader, A.: Thermostability in rubredoxin and its relationship to mechanical rigidity. Phys. Biol. 7, 016002 (2010)CrossRefGoogle Scholar
  11. 11.
    Rader, A., Anderson, G., Isin, B., Khorana, H., Bahar, I., Klein-Seetharaman, J.: Identification of core amino acids stabilizing rhodoposin. PNAS 101, 7246–7251 (2004)CrossRefGoogle Scholar
  12. 12.
    Rader, A.J., Hespenheide, B.M., Kuhn, L.A., Thorpe, M.F.: Protein unfolding: rigidity lost. Proc. Nat. Acad. Sci. 99(6), 3540–3545 (2002)CrossRefGoogle Scholar
  13. 13.
    Streinu, I.: Large scale rigidity-based flexibility analysis of biomolecules. Struct. Dyn. 3, 012005 (2016)CrossRefGoogle Scholar
  14. 14.
    Wells, S., Jimenez-Roldan, J., Römer, R.: Comparative analysis of rigidity across protein families. Phys. Biol. 6, 046005 (2009)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  1. 1.Biomedical Informatics ProgramStanford UniversitySanta ClaraUSA
  2. 2.Department of Computer ScienceSmith CollegeNorthamptonUSA
  3. 3.School of Computer ScienceUniversity of Massachusetts AmherstAmherstUSA

Personalised recommendations