Projection methods for the analysis of complex motions in macromolecules

Molecular Simulation

Volumn 23, Issue 4-5, 2000, Pages 275-292

  Hinsen, Konrad ^a   Kneller, Gerald R ^a  

^a CENTRE DE BIOPHYSIQUE MOLÉCULAIRE   (France)

Author keywords

Normal modes; Protein dynamics; Trajectory analysis

Indexed keywords

EID: 0001739385     PISSN: 08927022     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (24)

1. Smith, J. C. (1991). "Protein dynamics: comparison of simulations with inelastic neutron scattering experiments", Q. Rev. Biophys., 24, 227-291.
2. Smith, J. C. and Kneller, G. R. (1993). "Combination of neutron scattering and molecular dynamics to determine internal motions in biomolecules", Mol. Sim., 10(2-6), 363-375.
3. Kneller, G. R. and Geiger, A. (1989). "A method to calculate the g-coefficients of the molecular pair correlation function from molecular dynamics simulations", Mol. Sim., 3, 283-300.
4. Kneller, G. R. (1991). "Superposition of molecular structures using quaternions", Mol. Sim., 7, 113-119.
5. Furois-Corbin, S., Smith, J. C. and Kneller, G. R. (1993). "Picosecond timescale rigid-helix and side-chain motions in deoxymyoglobin", Proteins, 16, 141-154.
6. Kneller, G. R. and Smith, J. C. (1994). "Liquid-like sidechain dynamics im myoglobin", J. Mol. Biol., 242, 181-195.
7. Go, N., Noguti, T. and Nishikawa, T. (1983). "Dynamics of a small protein in terms of low-frequency vibrational modes", Proc. Nat. Acad. Sci. U.S.A., 80, 3696-3700.
8. Lagant, P., Vergoten, G., Fleury, G. and Loucheux-Lefebvre, M.-H. (1984). "Raman spectroscopy and normal vibrations of peptides", Eur. J. Biochem., 139, 137-148.
9. Schulz, G. E. (1991). "Domain motions in proteins", Curr. Opin. Struct. Biol., 1, 883-888.
10. Hinsen, K., Thomas, A. and Field, M. J. (1999). "Analysis of domain motions in large proteins", Proteins, 34, 369-382.
11. Smith, J. C., Cusack, S., Pezzeca, U., Brooks, B. and Karplus, M. (1986). "Inelastic neutron scattering analysis of low frequency motion in proteins: A normal mode study of the bovine pancreatic trypsin inhibitor", J. Chem. Phys., 85, 3636-3654.
12. Smith, J. C., Cusack, S., Tidor, B. and Karplus, M. (1990). "Inelastic neutron scattering analysis of low-frequency motions in proteins: Harmonic and damped harmonic models of bovine pancreatic trypsin inhibitor", J. Chem. Phys., 93, 2974-2991.
13. Kitao, A. and Go, N. (1999). "Investigating protein dynamics in collective coordinate space", Curr. Opin. Struct. Biol., 9, 164-169.
14. Press, W. H., Teukolsky, S. A., Vetterling, W. T. and Flannery, B. P., Numerical Recipes in C, 2nd edition, Cambridge University Press, Cambridge, 1992.
15. Anderson, E., Bai, Z., Bischof, C., Demmel, J. W., Dongarra, J. J., du Croz, J., Greenbaum, A., Hammarling, S., McKenney, A. and Sorensen, D., "LAPACK: A portable linear algebra library for high-performance computers", Computer Science Dept. Technical Report CS-90-105, University of Tennessee, Knoxville, 1990.
16. Hinsen, K., "The Molecular Modeling Toolkit: A case study of a large scientific application in Python", Proceedings of the 6th International Python Conference, http:// www.python.org/workshops/1997-10/proceedings/hinsen.html
17. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M. Jr., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W. and Kollman, P. A. (1995). "A second generation force field for the simulation of proteins and nucleic acids", J. Am. Chem. Soc., 117, 5179-5197.
18. Ansari, A. (1999). "Langevin modes analysis of myoglobin", J. Chem. Phys., 110, 1774-1780.
19. Rahman, A., Singwi, K. S. and Sjölander, A. (1962). "Theory of Slow Neutron Scattering. I", Phys. Rev., 126, 986-996.
20. Brooks, C. L., Karplus, M. and Pettit, B. M. (1988). "Proteins, a theoretical perspective of dynamics, structure, and thermodynamics", Adv. Chem. Phys., 71.
21. Settles, M. and Doster, W., "Iterative calculation of the vibrational density of states from incoherent neutron scattering data with the account of double scattering", In: Biological Macromolecular Dynamics, Eds., Cusack, S., Büttner, H., Ferrand, M., Langan, P. and Timmins, P., Adenine Press, New York, 1997.
22. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. and Karplus, M. (1983). "CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations", J. Comp. Chem., 4, 187-217.
23. Lovesey, S., "Theory of neutron scattering from condensed matter", Vol.1, Clarendon Press, Oxford, 1984.
24. Hinsen, K. (1998). "Analysis of domain motions by approximate normal mode calculations", Proteins, 33, 417-429.