The eNMR platform for structural biology

Journal of Structural and Functional Genomics

Volumn 11, Issue 1, 2010, Pages 1-8

  Bonvin, Alexandre M J J ^a   Rosato, Antonio ^b   Wassenaar, Tsjerk A ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

^b UNIVERSITY OF FLORENCE   (Italy)

Author keywords

Casd NMR; CS rosetta; Cyana; Haddock; NMR; Xplor NIH

Indexed keywords

ACCESS TO INFORMATION; BIOMEDICINE; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA ANALYSIS; EUROPE; INFORMATION PROCESSING; INTERNET; MONTE CARLO METHOD; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; REVIEW; STRUCTURE ANALYSIS;

BIOLOGICAL SCIENCE DISCIPLINES; INTERNET; MAGNETIC RESONANCE SPECTROSCOPY; MOLECULAR BIOLOGY; SOFTWARE;

MELANOGRAMMUS;

EID: 77949429714     PISSN: 1345711X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10969-010-9084-9     Document Type: Review

References (25)

1. L Banci I Bertini G Cavallaro A Giachetti C Luchinat G Parigi 2004 Paramagnetism-based restraints for Xplor-NIH J Biomol NMR 28 249 261 10.1023/B:JNMR.0000013703.30623.f7 1:CAS:528:DC%2BD2cXnsFCqtQ%3D%3D 14752258 (Pubitemid 38220173)
2. HM Berman J Westbrook Z Feng G Gilliland TN Bhat H Weissig IN Shindyalov PE Bourne 2000 The Protein Data Bank Nucleic Acids Res 28 235 242 10.1093/nar/28.1.235 1:CAS:528:DC%2BD3cXhvVKjt7w%3D 10592235
3. I Bertini C Luchinat G Parigi R Pierattelli 2008 Perspectives in NMR of paramagnetic proteins Dalton Trans 2008 3782 3790 10.1039/b719526e
4. M Billeter G Wagner K Wüthrich 2008 Solution NMR structure determination of proteins revisited J Biomol NMR 42 155 158 10.1007/s10858-008- 9277-8 1:CAS:528:DC%2BD1cXht1KrsbvO 18827972
5. Case DA, Darden TA, Cheatham TE, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Wang B, Pearlman DA, Crowley M, Brozell S, TsuiV, Gohlke H, Mongan J, HornakV, Cui G, Beroza P, Schafmeister CE, Caldwell JW, Ross WS, Kollman PA (2008) AMBER 10. University of California, San Francisco, CA
6. SJ De Vries AD Van Dijk M Krzeminski M Van Dijk A Thureau V Hsu T Wassenaar AM Bonvin 2007 HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets Proteins 69 726 733 10.1002/prot.21723 17803234 (Pubitemid 350210131)
7. C Dominguez R Boelens AM Bonvin 2003 HADDOCK: a protein-protein docking approach based on biochemical or biophysical information J Am Chem Soc 125 1731 1737 10.1021/ja026939x 1:CAS:528:DC%2BD3sXkvFGquw%3D%3D 12580598 (Pubitemid 36232568)
8. P Guntert 2009 Automated structure determination from NMR spectra Eur Biophys J 38 129 143 10.1007/s00249-008-0367-z 18807026
9. P Güntert C Mumenthaler K Wüthrich 1997 Torsion angle dynamics for NMR structure calculation with the new program DYANA J Mol Biol 273 283 298 10.1006/jmbi.1997.1284 9367762 (Pubitemid 27460230)
10. T Herrmann P Güntert K Wüthrich 2002 Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA J Mol Biol 319 209 227 10.1016/S0022-2836(02)00241-3 1:CAS:528:DC%2BD38XktlGktLo%3D 12051947 (Pubitemid 34729497)
11. T Ikegami L Verdier P Sakhaii S Grimme P Pescatore K Saxena KM Fiebig C Griesinger 2004 Novel techniques for weak alignment of proteins in solution using chemical tags coordinating lanthanide ions J Biomol NMR 29 339 349 10.1023/B:JNMR.0000032611.72827.de 1:CAS:528:DC%2BD2cXltVGnsLg%3D 15213432 (Pubitemid 38864832)
12. J Janin K Henrick J Moult LT Eyck MJ Sternberg S Vajda I Vakser SJ Wodak 2003 CAPRI: a critical assessment of PRedicted interactions Proteins 52 2 9 10.1002/prot.10381 1:CAS:528:DC%2BD3sXkslahsr4%3D 12784359 (Pubitemid 36648842)
13. MF Lensink R Mendez SJ Wodak 2007 Docking and scoring protein complexes: CAPRI 3rd Edition Proteins 69 704 718 10.1002/prot.21804 1:CAS:528: DC%2BD2sXhtl2qsb3E 17918726 (Pubitemid 350214359)
14. A Mittermaier LE Kay 2006 New tools provide new insights in NMR studies of protein dynamics Science 312 224 228 10.1126/science.1124964 1:CAS:528:DC%2BD28XjtlOjs7o%3D 16614210
15. J Moult JT Pedersen R Judson K Fidelis 1995 A large-scale experiment to assess protein structure prediction methods Proteins 23 ii iv 10.1002/prot.340230303 1:STN:280:DyaK287oslCntw%3D%3D 8710822
16. G Pintacuda M John XC Su G Otting 2007 NMR structure determination of protein-ligand complexes by lanthanide labeling Acc Chem Res 40 206 212 10.1021/ar050087z 1:CAS:528:DC%2BD2sXjtVaqtg%3D%3D 17370992
17. CA Rohl CE Strauss KM Misura D Baker 2004 Protein structure prediction using Rosetta Methods Enzymol 383 66 93 10.1016/S0076-6879(04)83004-0 1:CAS:528:DC%2BD2cXkt1Siurs%3D 15063647 (Pubitemid 38401787)
18. A Rosato A Bagaria D Baker B Bardiaux A Cavalli JF Doreleijers A Giachetti P Guerry P Guntert T Herrmann YJ Huang HR Jonker B Mao TE Malliavin GT Montelione M Nilges S Raman SG Van der WF Vranken GW Vuister AM Bonvin 2009 CASD-NMR: critical assessment of automated structure determination by NMR Nat Methods 6 625 626 10.1038/nmeth0909-625 1:CAS:528:DC%2BD1MXhtVKjsbnI 19718014
19. CD Schwieters J Kuszewski N Tjandra GM Clore 2003 The Xplor-NIH NMR molecular structure determination package J Magn Reson 160 65 73 10.1016/S1090-7807(02)00014-9 1:CAS:528:DC%2BD3sXmslaquw%3D%3D 12565051
20. Y Shen A Bax 2007 Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology J Biomol NMR 38 289 302 10.1007/s10858-007-9166-6 1:CAS:528:DC%2BD2sXotVantbg%3D 17610132 (Pubitemid 47108511)
21. Y Shen O Lange F Delaglio P Rossi JM Aramini G Liu A Eletsky Y Wu KK Singarapu A Lemak A Ignatchenko CH Arrowsmith T Szyperski GT Montelione D Baker A Bax 2008 Consistent blind protein structure generation from NMR chemical shift data Proc Natl Acad Sci USA 105 4685 4690 10.1073/pnas.0800256105 1:CAS:528:DC%2BD1cXkt12qs7Y%3D 18326625 (Pubitemid 351753807)
22. Y Shen R Vernon D Baker A Bax 2009 De novo protein structure generation from incomplete chemical shift assignments J Biomol NMR 43 63 78 10.1007/s10858-008-9288-5 1:CAS:528:DC%2BD1MXhsVOktw%3D%3D 19034676
23. WF Vranken W Boucher TJ Stevens RH Fogh A Pajon M Llinas EL Ulrich JL Markley J Ionides ED Laue 2005 The CCPN data model for NMR spectrooscopy development of a software pipeline Proteins 59 687 696 10.1002/prot.20449 1:CAS:528:DC%2BD2MXksVKmt7c%3D 15815974 (Pubitemid 40695845)
24. J Wöhnert KJ Franz M Nitz B Imperiali H Schwalbe 2003 Protein alignment by a coexpressed lanthanide-binding tag for the measurement of residual dipolar couplings J Am Chem Soc 125 13338 13339 10.1021/ja036022d 14583012 (Pubitemid 37352103)
25. Wüthrich K (1986) NMR of proteins and nucleic acids. Wiley, New York