Ab-initio protein folding using molecular dynamics and a simplified off-lattice model

Journal of Bionanoscience

Volumn 7, Issue 4, 2013, Pages 391-402

  Benítez, César M V ^a   Lopes, Heitor Silvério ^a  

^a UNIVERSIDADE TECNOLÓGICA FEDERAL DO PARANÁ   (Brazil)

Author keywords

3D AB model; Molecular dynamics; Protein folding problem

Indexed keywords

AB INITIO; BIOLOGICAL FEATURES; GLOBULAR PROTEINS; HYDROPHOBIC CORE; OFF-LATTICE MODELS; PARALLEL PROCESSING; PROTEIN FOLDING PROBLEM; SYNTHETIC SEQUENCE;

CRYSTAL LATTICES; MOLECULAR DYNAMICS; PROTEIN FOLDING; PROTEINS; THREE DIMENSIONAL COMPUTER GRAPHICS;

THREE DIMENSIONAL;

EID: 84886930672     PISSN: 15577910     EISSN: 15577929     Source Type: Journal    
DOI: 10.1166/jbns.2013.1153     Document Type: Article

References (41)

1. L. Luheshi and C. Dobson, FEBS Lett. 583, 2581 (2009).
2. S. Broadley and F. U. Hartl, FEBS Lett. 583, 2647 (2009).
3. Y. Chen, F. Ding, H. Nie, A. W. Serohijos, S. Sharma, K. Wilcox, S. Yin, and N. D. Dokholyan, Arch. Biochem. Biophys. 469, 4 (2008).
4. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. P. E. Bourne, Nucleic Acids Res. 28, 235 (2000).
5. C. B. Anfinsen, Science 181, 223 (1973).
6. K. Dill, S. Ozkan, M. Shell, and T. Weikl, Annual Review of Biophysics 37, 289 (2008).
7. V. Nanda and R. Koder, Nature Chemistry 2, 15 (2010).
8. D. Röthlisberger, O. Khersonsky, A. Wollacott, L. Jiang, J. DeChancie, J. Betker, J. Gallaher, E. Althoff, A. Zanghellini, O. Dym, S. Albeck, K. Houk, D. Tawfik, and D. Baker, Nature 453, 190 (2008).
9. R. Broglia and G. Tiana, Physical models for protein folding and drug design, Proceedings Idea-Finding Symposium, Frankfurt Institute for Advanced Studies, Frankfurt, Germany (2003), pp. 23-33.
10. G. Nicosia and G. Stracquadanio, Biophys. J. 95, 4988 (2008).
11. H. S. Lopes, Evolutionary algorithms for the protein folding problem: A review and current trends, Computational Intelligence in Biomedicine and Bioinformatics, Springer-Verlag, Heidelberg (2008), Vol. I, pp. 297-315.
12. A. Liwo, M. Khalili, and H. A. Scheraga, Ab-initio simulations of protein-folding pathways by molecular dynamics with the unitedresidue model of polypeptide chains, Proceedings of the National Academy of Sciences, 102, 2362 (2005).
13. R. Day and V. Daggett, Adv. Protein Chem. 66, 373 (2003).
14. D. Baker, Nature 405, 39 (2000).
15. Z. Cui, D. Liu, J. Zeng, and Z. Shi, Journal of Computational and Theoretical Nanoscience 9, 2255 (2012).
16. H. S. Lopes, Evolutionary algorithms for the protein folding problem: A review and current trends, Computational Intelligence in Biomedicine and Bioinformatics, Springer-Verlag, Heidelberg (2008), Vol. I, pp. 297-315.
17. M. Karplus, Fold Des. 2, S69 (1997).
18. M. Gruebele, Current Opinion in Structural Biology 12, 161 (2002).
19. F. Stillinger and T. Head-Gordon, Physical Review E 52, 2872 (1995).
20. A. Irback, C. Peterson, F. Potthast, and O. Sommelius, J. Chem. Phys. 1, 273 (1997).
21. D. Rapaport, The Art of Molecular Dynamics Simulation, Cambridge University Press, Cambridge, UK (2004).
22. T. Harder, M. Borg, S. Bottaro, W. Boomsma, S. Olsson, and J. Ferkinghoff-Borg, Structure 20, 1028 (2012).
23. N. Nouri and S. Ziaei-Rad, Journal of Computational and Theoretical Nanoscience 9, 2144 (2012).
24. G. Marsaglia, The Annals of Mathematical Statistics 43, 645 (1972).
25. D. Knuth, The Art of Computer Programming, Addison-Wesley, USA (1981), Vol. 2.
26. W. C. Swope, H. C. Andersen, P. H. Berens, and K. R. Wilson, The Journal of Chemical Physics 76, 637 (1982).
27. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gusteren, A. DiNola, and J. R. Haak, J. Chem. Phys. 81, 3684 (1984).
28. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, Journal of Computational Physics 23, 327 (1977).
29. H. S. Lopes and M. P. Scapin, A hybrid genetic algorithm for the protein folding problem using the 2D-HP lattice model, Success in Evolutionary Computation, ser. Studies in Computational Intelligence, edited by A. Yang, Y. Shan, and L. T. Bui, Springer-Verlag, Berlin, Germany (2008), Vol. 92, pp. 121-140.
30. D. Frenkel and B. Smit, Understanding Molecular Simulation. From Algorithms to Applications, Academic Press, San Diego, USA (2002).
31. C. M. V. Benítez and H. S. Lopes, Hierarchical parallel genetic algorithm applied to the three-dimensional HP side-chain protein folding problem, Proceedings of the IEEE International Conference on Systems, Man and Cybernetics. IEEE Press, Piscataway, USA (2010).
32. K. Yue and K. Dill, Physical Review E 48, 2267 (1993).
33. B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter, Molecular Biology of the Cell, Garland Science, New York, USA (2002).
34. M. Mann, R. Saunders, C. Smith, R. Backofen, and C. Deane, Advances in Bioinformatics 2012, 148045 (2012).
35. W. Kabsch, Acta Crystallographica A34, 827 (1978).
36. R. Unger, The building block approach to protein structure prediction, ser. Cellular Origin, Life in Extreme Habitats and Astrobiology, edited by J. Seckbach and E. Rubin, Kluwer Academic, Amsterdam, The Netherlands (2004), Vol. 8, pp. 177-188.
37. M. Marti-Renom, B. Yerkovich, and A. Sali, Comparative protein structure prediction, Current Protocols in Protein Science, John Wiley & Sons, New York, USA (2001).
38. M. Olivella, X. Deupi, C. Govaerts, and L. Pardo, Biophys. J. 82, 3207 (2002).
39. A. Ramanathan and P. Agarwal, J. Phys. Chem. B 113, 16 669 (2009).
40. C. Vehlow, H. Stehr, M. Winkelmann, J. Duarte, L. Petzold, J. Dense, and M. Lappe, Bioinformatics 27, 1573 (2011).
41. N. B. Armstrong Junior, H. S. Lopes, and C. R. E. Lima, Preliminary steps towards protein folding prediction using reconfigurable computing, Proceedings 3rd International Conference on Reconfigurable Computing and FPGAs, IEEE, Piscataway, USA (2006), pp. 92-98.