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All issues Volume 6 / No 6 (2011) Math. Model. Nat. Phenom., 6 6 (2011) 278-294 References
Free Access
Issue
Math. Model. Nat. Phenom.
Volume 6, Number 6, 2011
Biomathematics Education
Page(s) 278 - 294
Section Continuous Modeling
DOI https://doi.org/10.1051/mmnp/20116615
Published online 05 October 2011
  1. A. Atilgan, S. Durell, R. Jernigan, M. Demirel, O. Keskin, and I. Bahar. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophysical Journal, 80 (2001), 505–515. [CrossRef] [PubMed] [Google Scholar]
  2. I. Bahar, A. R. Atilgan, and B. Erman. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Folding and Design, 2 (1997), 173–181. [Google Scholar]
  3. I. Bahar and A. Rader. Coarse-grained normal mode analysis in structural biology. Current Opinion in Structural Biology, 15 (2005), 586–592. [CrossRef] [PubMed] [Google Scholar]
  4. Q. Cui and I. Bahar. Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems. Chapman and Hall/CRC, 1 ed., 2005. [Google Scholar]
  5. J. L. Dunn. A pictorial visualization of normal mode vibrations of the fullerene (C60) molecule in terms of vibrations of a hollow sphere. Journal of Chemical Education, 87 (2010), 819–822. [CrossRef] [Google Scholar]
  6. D. A. Kondrashov, Q. Cui, and G. N. Phillips, Jr. Optimization and evaluation of a coarse-grained model of protein motion using X-Ray crystal data. Biophysical Journal, 91 (2006), 2760–2767. [Google Scholar]
  7. D. A. Kondrashov, A. W. Van Wynsberghe, R. M. Bannenl, Q. Cui, and G. N. Phillips, Jr. Protein structural variation in computational models and crystallographic data. Structure, 15 (2007), 169–177. [CrossRef] [PubMed] [Google Scholar]
  8. W. G. Krebs, V. Alexandrov, C. A. Wilson, N. Echols, H. Yu, and M. Gerstein. Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic. Proteins: Structure, Function, and Genetics, 48 (2002), 682–695. [CrossRef] [Google Scholar]
  9. L. Orellana, M. Rueda, C. Ferrer-Costa, J. Lopez-Blanco, P. Chacon, and M. Orozco. Approaching elastic network models to molecular dynamics flexibility. Journal of Chemical Theory and Computation, 6 (2010), 2910–2923. [CrossRef] [PubMed] [Google Scholar]
  10. W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery. Numerical recipes: The art of scientific computing. Cambridge University Press, Cambridge, 3rd ed, 2007. [Google Scholar]
  11. K. Suhre and Y. Sanejouand. Elnemo: A normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Research, 32 (2004), W610–W614. [CrossRef] [PubMed] [Google Scholar]
  12. M. M. Tirion. Large-amplitude elastic motions in proteins from a single-parameter atomic analysis. Physical Review Letters, 77 (1996), 1905–1915. [Google Scholar]
  13. A. W. Van Wynsberghe and Q. Cui. Interpreting correlated motions using normal mode analysis. Structure, 14 (2006), 1647–1653. [CrossRef] [PubMed] [Google Scholar]
  14. L. Yang and I. Bahar. Coupling between catalytic site and collective dynamics: A requirement for mechanochemical activity of enzymes. Structure, 13 (2005), 893–904. [CrossRef] [PubMed] [Google Scholar]
  15. L. Yang, X. Liu, C. J. Jursa, M. Holliman, A. Rader, H. A. Karimi, and I. Bahar. iGNM: A database of protein functional motions based on gaussian network model. Bioinformatics, 21 (2005), 2978 –2987. [CrossRef] [PubMed] [Google Scholar]

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