Assessing precision and accuracy of protein structures derived from NMR data

Proteins: Structure, Function and Genetics

Volumn 59, Issue 4, 2005, Pages 655-661

  Snyder, David A ^b   Bhattacharya, Aneerban ^b   Huang, Yuanpeng J ^b   Montelione, Gaetano T ^a  

^a RUTGERS UNIVERSITY   (United States)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ACCURACY; ALGORITHM; ATOMIC PARTICLE; CRYSTAL STRUCTURE; EDITORIAL; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN QUALITY; PROTEIN STRUCTURE; REPRODUCIBILITY; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING; VALIDATION PROCESS; X RAY ANALYSIS;

DATABASES, PROTEIN; MAGNETIC RESONANCE SPECTROSCOPY; PROTEINS; REPRODUCIBILITY OF RESULTS;

EID: 18844433630     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20499     Document Type: Editorial

References (27)

1. Taylor JR. An introduction to error analysis. Sausalito, CA: University Science Books; 1982. 270 p.
2. García AE, Krumhansl JA, Frauenfelder H. Variations on a theme by Debye and Waller: from simple crystals to proteins. Proteins 1997;29:153-160.
3. Nabuurs SB, Spronk CAEM, Krieger E, Maassen H, Vriend G, Vuister GW. Quantitative evaluation of experimental NMR restraints. J Am Chem Soc 2003;125:12026-12034.
4. Clore GM, Gronenborn AM. Structures of larger proteins in solution: three- and four-dimensional heteronuclear NMR spectroscopy. Science 1991;252:1390-1399.
5. Clore GM, Gronenborn AM. Structures of larger proteins, protein-ligand and protein-DNA complexes by multidimensional heteronuclear NMR. Protein Sci 1994;3:372-390.
6. Grishaev A, Llinas M. CLOUDS, a protocol for deriving a molecular proton density via NMR. Proc Natl Acad Sci USA 2002;99:6707-6712.
7. Grishaev A, Llinas M. Protein structure elucidation from NMR proton densities. Proc Natl Acad Sci USA 2002;99:6713-6718.
8. Habeck M, Rieping W, Nilges M. Estimation of protein configurations from NOESY spectra. AIP Conference Proceedings, Vol 735. Melville, NY: Amer Inst Phys; 2004. p 119-126.
9. Kelley LA, Gardner SP, Sutcliffe MJ. An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures. Protein Eng 1997;10:737-741.
10. H domains of immunoglobin molecules. Protein Eng 1998;11:1015-1025.
11. Gerstein M, Altman RB. Using a measure of structural variation to define a core for the globins. Comput Appl Biosci 1995;11:633-644.
12. Spronk CAEM, Nabuurs SB, Bonvin AMJJ, Krieger E, Vuister GW, Vriend G. The precision of NMR structure ensembles revisited. J Biomol NMR 2003;25:225-234.
13. Tejero R, Bassolino-Klimas D, Bruccoleri RE, Montelione GT. Application of simulated annealing with restricted molecular dynamics using CONGEN: energy refinement of the NMR solution structures of epidermal and type-alpha transforming growth factors. Protein Sci 1996;5:578-592.
14. Bonvin AMJJ, Brünger AT. Conformational variability of solution nuclear magnetic resonance studies. J Mol Biol 1995;250:80-93.
15. Torda AE, Scheek RM, van Gunsteren WF. Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat. J Mol Biol 1990;214:223-235.
16. Hyberts SG, Goldberg MS, Havel TF, Wagner G. The solution structure of eglin C based on measurements of many NOEs and coupling constants and its comparison with X-ray structures. Protein Sci 1992;1:736-751.
17. Word JM, Bateman RC, Presley BK, Lovell SC, Richardson DC. Exploring steric constraints on protein mutations using MAGE/PROBE. Protein Sci 2000;9:2251-2259.
18. Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, Richardson DC. Visualizing and quantifying molecular goodness of fit: small-probe contact dots with explicit hydrogen atoms. J Mol Biol 1999;285:1711-1733.
19. Laskowski RA, Rullmann JA, MacArthur MW, Kaptein R, Thornton JM. AQUA and PROCHECK NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 1996;8:477-486.
20. Hooft RW, Vriend G, Sander C, Abola EE. Errors in protein structures. Nature 1996;381:272.
21. Grishaev A, Bax A. An empirical backbone-backbone hydrogen-bonding potential in proteins and its applications to NMR structure refinement and validation. J Am Chem Soc 2004;126:7281-7292.
22. Bhattacharya A, Montelione GT. PSVS: a Protein Structure Validation Suite for structures derived from NMR or homology modeling. 2005. Manuscript in preparation.
23. Garbuzynskiy SO, Melnik BS, Lobanov MY, Finkelstein AV, Galzitskaya OV. Comparison of X-ray and NMR structures: Is there a systematic difference in residue contacts between X-ray and NMR-resolved protein structures? Proteins 2005. Forthcoming.
24. Gronwald W, Kirchhofer R, Gorler A, Kremer W, Ganslmeier B, Neidig KP, Kalbitzer HR. RFAC, a program for automated NMR R-factor estimation. J Biomol NMR 2000;17:137-151.
25. Huang YJ, Powers R, Montelione GT. Protein NMR recall, precision and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. J Am Chem Soc 2005;127:1665-1674.
26. Bax A. Weak alignment offers new NMR opportunities to study protein structure and dynamics. Protein Sci 2003;12:1-16.
27. Prestegard JH, Bougault CM, Kishore AI. Residual dipolar couplings in structure determination of biomolecules. Chem Rev 2004;104:3519-3540.