The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions

Journal of Computational Chemistry

Volumn 27, Issue 3, 2006, Pages 316-325

  Wassenaar, Tsjerk A ^a   Mark, Alan E ^a,b  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

MANOVA; Molecular dynamics; Near densest lattice packing; Periodic boundary conditions; Simulation

Indexed keywords

BOUNDARY CONDITIONS; COMPUTER SIMULATION; CONSTRAINT THEORY; LATTICE CONSTANTS; MOLECULAR DYNAMICS;

MANOVA; NEAR-DENSEST LATTICE PACKING; PERIODIC BOUNDARY CONDITIONS;

PROTEINS;

PROTEIN;

ARTICLE; CHEMISTRY; PROTEIN CONFORMATION;

PROTEIN CONFORMATION; PROTEINS;

EID: 32344451982     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.20341     Document Type: Article

References (30)

1. Bekker, H.; Van den Berg, J. P.; Wassenaar, T. A. J Comput Chem 2004, 25, 1037.
2. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res 2000, 28, 235.
3. Bekker, H. J Comput Chem 1997, 18, 1930.
4. Voronoi, G. J Reine Angew Math 1908, 134, 198.
5. Amadei, A.; Chillemi, G.; Ceruso, M.A.; Grottesi, A.; DiNola, A. J Chem Phys 2000, 112, 9.
6. Amadei, A.; Linssen, A. B. M.; Berendsen, H. J. C. Proteins 1993, 17, 412.
7. Amadei, A.; Ceruso, M. A.; DiNola, A. Proteins 1999, 36, 419.
8. Miller, R. G. Beyond ANOVA: Basics of Applied Statistics; Chapman & Hall: Boca Raton, FL, 1997.
9. Chambers, J. M.; Hastie, T. J. Statistical models in S; Wadsworth & Brooks/Cole, Pacific Grove, CA, 1992.
10. Morrison, D. F. Multivariate Statistical Methods; McGraw-Hill Kogakusha Ltd.: Tokyo, 1976.
11. McPhalen, C. A.; James, M. N. G. Biochemistry 1987, 26, 261.
12. McDonnell, J. M.; Fushman, D.; Cahill, S. M.; Zhou, W.; Wolven, A.; Wilson, C. B.; Nelle, T. D.; Resh, M. D.; Wills, J.; Cowburn, D. J Mol Biol 1998, 279, 921.
13. Artymiuk, P. J.; Blake, C. C. F.; Rice, D. W.; Wilson, K. S. Acta Crystallogr B 1982, 38, 778.
14. Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Comp Phys Commun 1995, 91, 43.
15. Lindahl, E.; Hess, B.; van der Spoel, D. J Mol Model 2001, 7, 306.
16. van der Spoel, D.; van Buuren, A. R.; Apol, E.; Meulenhoff, P. J.; Tieleman, D. P.; Sijbers, A. L. T. M.; Hess, B.; Feenstra, K. A.; Lindahl, E.; van Drunen, R.; Berendsen, H. J. C. Gromacs User Manual Version 3.1; 2002. Nijenborgh 4, 9747 AG Groningen, The Netherlands. Internet: http://www.gromacs.org.
17. van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: GROMOS96 Manual and User Guide; BIOMOS b.v.: Zürich, 1996.
18. Schuler, L. D.; van Gunsteren, W. F. Mol Sim 2000, 25, 301.
19. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. In Intermolecular Forces; Pullman, B., Ed.; Reidel: Dordrecht, 1981, p 331.
20. Tironi, I. G.; Sperb, R.; Smith, P. E.; van Gunsteren, W. F. J Chem Phys 1995, 102, 5451.
21. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J Chem Phys 1984, 81, 3684.
22. Miyamoto, S.; Kollman, P. A. J Comp Chem 1992, 13, 952.
23. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J Comput Phys 1997, 23, 327.
24. Development Core Team, R: A language and environment for statistical computing; http://www.R-project.org, 2004.
25. Roy, S. N.; Bose, R. C. Ann Math Stat 1953, 24, 513.
26. Miller, R. G. Simultaneous Statistical Inference; Springer: Berlin, 1981.
27. Roy, S. N. Some aspects of multivariate analysis; John Wiley & Sons, Inc.: New York, 1957.
28. DeLano, W, L. The PyMOL Molecular Graphics System; DeLano Scientific: San Carlos, CA, 2002.
29. POV-Ray: The Persistence of Vision Raytracer, www.povray.org.
30. Gunasekaran, K.; Ma, B.; Nussinov, R. Proteins 2004, 57, 433.