NOEnet - Use of NOE networks for NMR resonance assignment of proteins with known 3D structure

Bioinformatics

Volumn 25, Issue 4, 2009, Pages 474-481

  Stratmann, Dirk ^a   Van Heijenoort, Carine ^a   Guittet, Eric ^a  

^a INSTITUT DE CHIMIE DES SUBSTANCES NATURELLES   (France)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ACCURACY; ALGORITHM; ARTICLE; COMPUTER PROGRAM; LIGAND BINDING; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; STRUCTURAL BIOINFORMATICS; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; DATABASES, PROTEIN; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEINS;

EID: 60149087377     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn638     Document Type: Article

References (28)

1. Apaydin,M. et al. (2008) Structure-based protein NMR assignments using native structural ensembles. J. Biomol. NMR, 40, 263-276.
2. Bailey-Kellogg,C. et al. (2000) The NOESY jigsaw: Automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data. J. Comput. Biol., 7, 537-558.
3. Baran,M. et al. (2004) Automated analysis of protein NMR assignments and structures. Chem. Rev., 104, 3541-3556.
4. Bartels,C. et al. (1996) Automated sequence-specific NMR assignment of homologous proteins using the program garant. J. Biomol. NMR, 7, 207-213.
5. Dechter,R. (2003) Constraint Processing. 1st edn. Morgan Kaufmann, San Franciso, CA.
6. Dobson,C.M. et al. (1984) Nuclear overhauser effects and the assignment of the proton NMR spectra of proteins. FEBS Lett., 176, 307-312.
7. Erdmann,M.A. and Rule,G.S. (2002) Rapid protein structure detection and assignment using residual dipolar couplings. Technical Report CMU-CS-02-195. School of Computer Science, Carnegie Mellon University, Pittsburgh, PA.
8. Garrett,D.S. et al. (1997a) Identification by NMR of the binding surface for the histidine-containing phosphocarrier protein hpr on the N-terminal domain of enzyme I of the Escherichia coli phosphotransferase system. Biochemistry, 36, 4393-4398.
9. Garrett,D.S. et al. (1997b) Solution structure of the 30 kDa N-terminal domain of enzyme I of the Escherichia coli phosphoenolpyruvate:sUgar phosphotransferase system by multidimensional NMR. Biochemistry, 36, 2517-2530.
10. Gronwald,W. et al. (1998) Camra: Chemical shift based computer aided protein NMR assignments. J. Biomol. NMR, 12, 395-405.
11. Hus,J.-C. et al. (2002) Assignment strategy for proteins with known structure. J. Magn. Reson., 157, 119-123.
12. Koradi,R. et al. (1996) Molmol: A program for display and analysis of macromolecular structures. J. Mol. Graph., 14, 51-5, 29-32.
13. Langmead,C.J. and Donald,B.R. (2004) An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments. J. Biomol. NMR, 29, 111-138.
14. Langmead,C.J. et al. (2004) A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments. J. Comput. Biol., 11, 277-298.
15. Liao,D.I. et al. (1996) The first step in sugar transport: Crystal structure of the amino terminal domain of enzyme I of the E. coli PEP: sugar phosphotransferase system and a model of the phosphotransfer complex with Hpr. Structure, 4, 861-872.
16. Morshauser,R.C. and Zuiderweg,E.R. (1999) High-resolution four-dimensional HMQC-NOESY-HSQC spectroscopy. J. Magn. Reson., 139, 232-239.
17. Moseley,H.N. and Montelione,G.T. (1999) Automated analysis of NMR assignments and structures for proteins. Curr. Opin. in Struct. Biol. 9, 635-642.
18. Neal,S. et al. (2003) Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts. J. Biomol. NMR, 26, 215-240.
19. Pintacuda,G. et al. (2004) Fast structure-based assignment of 15N HSQC spectra of selectively 15n-labeled paramagnetic proteins. J. Am. Chem. Soc., 126, 2963-2970.
20. Pons,J.L. and Delsuc,M.A. (1999) Rescue: An artificial neural network tool for the NMR spectral assignment of proteins. J. Biomol. NMR, 15, 15-26.
21. Pristovsek,P. and Franzoni,L. (2006) Stereospecific assignments of protein NMR resonances based on the tertiary structure and 2D/3D NOE data. J. Comput. Chem., 27, 791-797.
22. Pristovsek,P. et al. (2002) Semiautomatic sequence-specific assignment of proteins based on the tertiary structure-the program st2nmr. J. Comput. Chem., 23, 335-340.
23. Sedgewick,R. (2002) Algorithms in C++ Part 5: Graph Algorithms. 3rd edn. Addison-Wesley Professional, San Francisco, CA.
24. Shen,Y. and Bax,A. (2007) Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology. J. Biomol. NMR, 38, 289-302.
25. Shen,Y. et al. (2005) G-matrix fourier transform noesy-based protocol for high-quality protein structure determination. J. Am. Chem. Soc., 127, 9085-9099.
26. Wüthrich,K. (1986) NMR of Proteins and Nucleic Acids. 1st edn. Wiley-Interscience, New York, NY.
27. Xiong,F. and Bailey-Kellogg,C. (2007) A hierarchical grow-and-match algorithm for backbone resonance assignments given 3D structure. In Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007, BIBE 2007, Boston, MA, pp. 403-410.
28. Xiong,F. et al. (2008) Contact replacement for NMR resonance assignment. Bioinformatics, 24, i205-i213.