C++ OPPS, a new software for the interpretation of protein dynamics from nuclear magnetic resonance measurements

International Journal of Quantum Chemistry

Volumn 110, Issue 2, 2010, Pages 387-405

  Zerbetto, Mirco ^a,b   Polimeno, Antonino ^a,b   Meirovitch, E V A ^a,b  

^a UNIVERSITY OF PADOVA   (Italy)

^b BAR ILAN UNIVERSITY   (Israel)

Author keywords

Dissipative properties; Nuclear magnetic resonance; Proteins; Slowly relaxing local structure; Stochastic modelling

Indexed keywords

ARGONNE NATIONAL LABORATORY; BASIC LINEAR ALGEBRA SUBPROGRAMS; C++ LANGUAGE; CHEMICAL SHIFT ANISOTROPY; COMMAND LINE; COMPLEX MATHEMATICS; CROSS CORRELATIONS; DIFFUSION TENSOR; DISSIPATIVE PROPERTIES; DYNAMICAL MODEL; FORTRAN 77; LOCAL STRUCTURE; MATRIX-VECTOR; MESSAGE PASSING INTERFACE; MICROSCOPIC PROPERTIES; NMR DATA; NMR RELAXATION; NUCLEAR MAGNETISM; NUCLEAR SPIN RELAXATION; OXFORD UNIVERSITY; PARALLELIZATIONS; PORTABLE IMPLEMENTATION; PROTEIN DYNAMICS; QUADRUPOLAR INTERACTIONS; STOCHASTIC MODELLING;

BIOCHEMISTRY; CHEMICAL SHIFT; COMPLEXATION; COMPUTATIONAL CHEMISTRY; COMPUTER SOFTWARE; GRAPHICAL USER INTERFACES; INTERFACES (COMPUTER); JAVA PROGRAMMING LANGUAGE; MAGNETISM; MESSAGE PASSING; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRESSES (MACHINE TOOLS); PROGRAM INTERPRETERS; PROTEINS; RELAXATION PROCESSES; SPECTRAL DENSITY; SPIN DYNAMICS; STOCHASTIC SYSTEMS; TENSORS;

RESONANCE;

EID: 75749157816     PISSN: 00207608     EISSN: 1097461X     Source Type: Journal    
DOI: 10.1002/qua.22289     Document Type: Conference Paper

References (25)

1. Palmer A. G., III. Annu Rev Biophys Biomol Struct 2001, 20, 129.
2. Lipari, G.; Szabo, A. J Am Chem Soc 1982, 104, 4546.
3. Lipari, G.; Szabo, A. J Am Chem Soc 1982, 104, 4559.
4. Polimeno, A.; Freed, J. H. Adv Chem Phys 1993, 83, 89.
5. Polimeno, A.; Freed, J. H. J Phys Chem 1995, 99, 10995.
6. Sastry, V. S. S.; Polimeno, A.; Crepeau, R. H.; Freed, J.H.J Chem Phys 1996, 105, 5753.
7. Earle, K. A.; Moscicki, J. K.; Polimeno, A.; Freed, J. H. J Chem Phys 1997,106, 9996.
8. Shapiro, Y. E.; Kahana, E.; Tugarinov, V.; Liang, Z.; Freed, J. H.; Meirovitch, E. Biochemistry 2002, 41, 6271.
9. Meirovitch, E.; Polimeno, A.; Freed, J. H. J Phys Chem B 2006, 110, 20615.
10. Meirovitch, E.; Polimeno, A.; Freed, J. H. J Phys Chem B 2007, 111, 12865.
11. Meirovitch, E.; Shapiro, Y. E.; Polimeno, A.; Freed, J. H. J Phys Chem A 2006, 110, 8366.
12. Abragam, A. The Principles of Nuclear Magnetism; Oxford University Press: Clarendon, London, 1961.
13. Moro, G.; Freed, J. H. Large-Scale Eigenvalue Problems, Vol.127: Mathematical Studies Series; Elsevier: New York, 1986.
14. Moro, G.; Freed, J. H. J Chem Phys 1981, 74, 3757.
15. (a) Guha, R.; Howard, M. T.; Hutchison, G. R.; Murray-Rust, P.; Rzepa, H.; Steinbeck, C.; Wegner, J. K.; Willighagen, E. L. J Chem Inf Model 2006, 46, 991;
16. (b) The Open Babel Package, version 2.0.1. Available at: http://openbabel.sourceforge. net/.
17. Barone, V.; Polimeno, A.; Zerbetto, M. J Comput Chem 1987.
18. Moro, G. Chem Phys 19817, 118, 181.
19. Barone, V.; Brustolon, M.; Cimino, P.; Polimeno, A.; Zerbetto, M.; Zoleo, A. J Am Chem Soc 2006, 128, 15865.
20. Carlotto, S.; Cimino, P.; Zerbetto, M.; Franco, L.; Corvaja, C.; Crisma, M.; Forraaggio, F.; Toniolo, C.; Polimeno, A.; Barone, V. J Am Chem Soc 2007, 129, 11248.
21. Zerbetto, M.; Carlotto, S.; Polimeno, A.; Corvaja, C.; Franco, L.; Toniolo, C.; Formaggio, F.; Barone, V.; Cimino, P. J Phys Chem B 2007, 111, 2668.
22. Zerbetto, M.; Polimeno, A.; Cimino, P.; Barone, V. J Chem Phys 2008, 128, 024501.
23. Hermosilla, L.; Sieiro, C.; Calle, P.; Zerbetto, M.; Polimeno, A. J Phys Chem B 2008, 112, 11202.
24. Barone, V.; Polimeno, A. Phys Chem Chem Phys 2006, 8, 4609.
25. Press, W. H.; Teukolsky, S. A.; Vetterling, W T.; Flannery, B. P. Numerical Recipes in C: The Art of Scientific Computing; Cambridge University Press: New York, NY, USA, 1992.