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Implementing efficient concerted rotations using Mathematica and C code

  • Luca TubianaEmail author
  • Miroslav Jurásek
  • Ivan Coluzza
Open Access
Regular Article
Part of the following topical collections:
  1. Advances in Computational Methods for Soft Matter Systems

Abstract.

In this article we demonstrate a general and efficient metaprogramming implementation of concerted rotations using Mathematica. Concerted rotations allow the movement of a fixed portion of a polymer backbone with fixed bending angles, like a protein, while maintaining the correct geometry of the backbone and the initial and final points of the portion fixed. Our implementation uses Mathematica to generate a C code which is then wrapped in a library by a Python script. The user can modify the Mathematica notebook to generate a set of concerted rotations suited for a particular backbone geometry, without having to write the C code himself. The resulting code is highly optimized, performing on the order of thousands of operations per second.

Graphical abstract

Keywords

Topical issue: Advances in Computational Methods for Soft Matter Systems 

Notes

Acknowledgments

Open Access funding provided by University of Vienna.

References

  1. 1.
    Peter Tompa, Trends Biochem. Sci. 27, 527 (2002)CrossRefGoogle Scholar
  2. 2.
    H. Jane Dyson, Peter E. Wright, Nat. Rev. Mol. Cell Biol. 6, 197 (2005)CrossRefGoogle Scholar
  3. 3.
    Anthony L. Fink, Curr. Opin. Struct. Biol. 15, 35 (2005)CrossRefGoogle Scholar
  4. 4.
    Vladimir N. Uversky, A. Keith Dunker, Biochim. Biophys. Acta-Proteins Proteomics 1804, 1231 (2010)CrossRefGoogle Scholar
  5. 5.
    Predrag Kukic, Arvind Kannan, Maurits J.J. Dijkstra, Sanne Abeln, Carlo Camilloni, Michele Vendruscolo, PLoS Comput. Biol. 11, e1004435 (2015)CrossRefGoogle Scholar
  6. 6.
    Valentina Tozzini, Curr. Opin. Struct. Biol. 15, 144 (2005)CrossRefGoogle Scholar
  7. 7.
    Cecilia Clementi, Curr. Opin. Struct. Biol. 18, 10 (2008)CrossRefGoogle Scholar
  8. 8.
    Paul C. Whitford, Jeffrey K. Noel, Shachi Gosavi, Alexander Schug, Kevin Y. Sanbonmatsu, Jose N. Onuchic, Proteins: Struct. Funct. Bioinform. 75, 430 (2009)CrossRefGoogle Scholar
  9. 9.
    Adam Liwo, Stanisław Ołdziej, Cezary Czaplewski, Dana S. Kleinerman, Philip Blood, Harold A. Scheraga, J. Chem. Theory Comput. 6, 890 (2010)CrossRefGoogle Scholar
  10. 10.
    Gregory R. Bowman, Vincent A. Voelz, Vijay S. Pande, Curr. Opin. Struct. Biol. 21, 4 (2011)CrossRefGoogle Scholar
  11. 11.
    Ivan Coluzza, PLoS ONE 6, e20853 (2011)CrossRefGoogle Scholar
  12. 12.
    M.M. Lin, A.H. Zewail, Ann. Phys. 524, 379 (2012)CrossRefGoogle Scholar
  13. 13.
    W.G. Noid, J. Chem. Phys. 139, 090901 (2013)ADSCrossRefGoogle Scholar
  14. 14.
    James T. MacDonald, Lawrence A. Kelley, Paul S. Freemont, PLoS ONE 8, e65770 (2013)ADSCrossRefGoogle Scholar
  15. 15.
    Ivan Coluzza, PLoS ONE 9, e112852 (2014)CrossRefGoogle Scholar
  16. 16.
    Ivan Coluzza, J. Phys.: Condens. Matter 29, 143001 (2017)Google Scholar
  17. 17.
    B. Mehlig, A.L.C. Ferreira, D.W. Heermann, Phys. Lett. B 291, 151 (1992)ADSCrossRefGoogle Scholar
  18. 18.
    B.M. Forrest, U.W. Suter, J. Chem. Phys. 101, 2616 (1994)ADSCrossRefGoogle Scholar
  19. 19.
    Dmitry G. Gromov, Juan J. de Pablo, J. Chem. Phys. 103, 8247 (1995)ADSCrossRefGoogle Scholar
  20. 20.
    Anne Voegler Smith, Carol K. Hall, Proteins: Struct. Funct. Genet. 44, 344 (2001)CrossRefGoogle Scholar
  21. 21.
    F. Calvo, J.P.K. Doye, Phys. Rev. E 63, 0109021 (2001)Google Scholar
  22. 22.
    L.R. Dodd, T.D. Boone, D.N. Theodorou, Mol. Phys. 78, 961 (1993)ADSCrossRefGoogle Scholar
  23. 23.
    Daniel Hoffmann, Ernst-Walter Knapp, Eur. Biophys. J. 24, 387 (1996)CrossRefGoogle Scholar
  24. 24.
    G. Favrin, A. Irbäck, F. Sjunnesson, J. Chem. Phys. 114, 8154 (2001)ADSCrossRefGoogle Scholar
  25. 25.
    Jakob P. Ulmschneider, William L. Jorgensen, J. Chem. Phys. 118, 4261 (2003)ADSCrossRefGoogle Scholar
  26. 26.
    Evangelos A. Coutsias, Chaok Seok, Matthew P. Jacobson, Ken A. Dill, J. Comput. Chem. 25, 510 (2004)CrossRefGoogle Scholar
  27. 27.
    Marcos R. Betancourt, J. Chem. Phys. 123, 174905 (2005)ADSCrossRefGoogle Scholar
  28. 28.
    Daniel J. Mandell, Evangelos A. Coutsias, Tanja Kortemme, Nat. Methods 6, 551 (2009)CrossRefGoogle Scholar
  29. 29.
    Sandro Bottaro, Wouter Boomsma, Kristoffer E. Johansson, Christian Andreetta, Thomas Hamelryck, Jesper Ferkinghoff-Borg, J. Chem. Theory Comput. 8, 695 (2012)CrossRefGoogle Scholar
  30. 30.
    Amelie Stein, Tanja Kortemme, PLoS ONE 8, e63090 (2013)ADSCrossRefGoogle Scholar
  31. 31.
    Stefano Zamuner, Alex Rodriguez, Flavio Seno, Antonio Trovato, PLoS ONE 10, e0118342 (2015)CrossRefGoogle Scholar
  32. 32.
    Mathematica, Version 9.0, Wolfram Reasearch Inc., Champaign, IL, 2018Google Scholar
  33. 33.
    Luca Tubiana, Miroslav Jurasek, luca-tubiana/concerted_rotations:  https://doi.org/10.5281/zenodo.1183330 (February 2018)
  34. 34.
    Andrea Cavalli, Xavier Salvatella, Christopher M. Dobson, Michele Vendruscolo, Proc. Natl. Acad. Sci. U.S.A. 104, 9615 (2007)ADSCrossRefGoogle Scholar
  35. 35.
    Andrea Cavalli, Carlo Camilloni, Michele Vendruscolo, J. Chem. Phys. 138, 03B603 (2013)Google Scholar
  36. 36.
    T. Alwyn Jones, Soren Thirup, EMBO J. 5, 819 (1986)Google Scholar
  37. 37.
    Cristian Micheletti, Flavio Seno, Amos Maritan, Proteins: Struct. Funct. Bioinform. 40, 662 (2000)CrossRefGoogle Scholar
  38. 38.
    Alessandro Pandini et al., BMC Bioinform. 11, 97 (2010)CrossRefGoogle Scholar
  39. 39.
    Mark Galassi, Jim Davies, James Theiler, Brian Gough, Gerard Jungman, Patrick Alken, Michael Booth, Fabrice Rossi, GNU Scientific Library Reference Manual (Network Theory Ltd., 2001)Google Scholar
  40. 40.
    Frank J. Aherne, Neil A. Thacker, Peter I. Rockett, Kybernetika 34, 363 (1998)MathSciNetGoogle Scholar

Copyright information

© The Author(s) 2018

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Authors and Affiliations

  • Luca Tubiana
    • 1
    Email author
  • Miroslav Jurásek
    • 2
    • 3
  • Ivan Coluzza
    • 4
  1. 1.Computational Physics DepartmentUniversity of ViennaViennaAustria
  2. 2.Faculty of ScienceMasaryk UniversityBrnoCzech Republic
  3. 3.CEITEC - Central European Institute of TechnologyBrnoCzech Republic
  4. 4.CIC biomaGUNE Parque Cientfico y Tecnolgico de GipuzkoaDonostia / San Sebastin, GipuzkoaSpain

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