Recommendations of the wwPDB NMR validation task force

Structure

Volumn 21, Issue 9, 2013, Pages 1563-1570

  Montelione, Gaetano T ^a,b   Nilges, Michael ^d,e   Bax, Ad ^f   Güntert, Peter ^h,i   Herrmann, Torsten ^j,k   Richardson, Jane S ^l   Schwieters, Charles D ^g   Vranken, Wim F ^m,n   Vuister, Geerten W ^o   Wishart, David S ^p   Berman, Helen M ^c   Kleywegt, Gerard J ^q   Markley, John L ^r  

^a RUTGERS UNIVERSITY   (United States)

^b RUTGERS ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

^c RUTGERS UNIVERSITY   (United States)

^d INSTITUT PASTEUR   (France)

^e CNRS   (France)

^f NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^g NATIONAL INSTITUTES OF HEALTH   (United States)

^h GOETHE UNIVERSITY   (Germany)

ⁱ FRANKFURT INSTITUTE FOR ADVANCED STUDIES   (Germany)

^j UNIVERSITÉ DE LYON   (France)

^k Institut des Sciences Analytiques   (France)

^l DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^m DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

ⁿ VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

^o UNIVERSITY OF LEICESTER   (United Kingdom)

^p UNIVERSITY OF ALBERTA   (Canada)

^q EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^r UNIVERSITY OF WISCONSIN MADISON   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ANISOTROPY; ARTICLE; DATA BASE; INFORMATION PROCESSING; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTON NUCLEAR MAGNETIC RESONANCE; QUALITY CONTROL; STRUCTURAL EQUATION MODELING; VALIDATION STUDY; X RAY CRYSTALLOGRAPHY; X RAY DIFFRACTION;

ADVISORY COMMITTEES; DATABASES, PROTEIN; GUIDELINES AS TOPIC; KNOWLEDGE BASES; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEINS; QUALITY CONTROL; REFERENCE STANDARDS; VALIDATION STUDIES AS TOPIC;

EID: 84883476906     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2013.07.021     Document Type: Article

References (57)

1. M. Andrec, D.A. Snyder, Z. Zhou, J. Young, G.T. Montelione, and R.M. Levy A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing Proteins 69 2007 449 465
2. J.M. Aramini, D. Petrey, D.Y. Lee, H. Janjua, R. Xiao, T.B. Acton, J.K. Everett, and G.T. Montelione Solution NMR structure of Alr2454 from Nostoc sp. PCC 7120, the first structural representative of Pfam domain family PF11267 J. Struct. Funct. Genomics 13 2012 171 176
3. W.B. Arendall III, W. Tempel, J.S. Richardson, W. Zhou, S. Wang, I.W. Davis, Z.J. Liu, J.P. Rose, W.M. Carson, and M. Luo A test of enhancing model accuracy in high-throughput crystallography J. Struct. Funct. Genomics 6 2005 1 11
4. A. Bagaria, V. Jaravine, Y.J. Huang, G.T. Montelione, and P. Güntert Protein structure validation by generalized linear model root-mean-square deviation prediction Protein Sci. 21 2012 229 238
5. H. Berman, K. Henrick, and H. Nakamura Announcing the worldwide Protein Data Bank Nat. Struct. Biol. 10 2003 980
6. H. Berman, K. Henrick, H. Nakamura, and J.L. Markley The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data Nucleic Acids Res. 35 2007 D301 D303
7. A. Bhattacharya, R. Tejero, and G.T. Montelione Evaluating protein structures determined by structural genomics consortia Proteins 66 2007 778 795
8. A.T. Brünger, G.M. Clore, A.M. Gronenborn, R. Saffrich, and M. Nilges Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation Science 261 1993 328 331
9. M. Bryson, F. Tian, J.H. Prestegard, and H. Valafar REDCRAFT: a tool for simultaneous characterization of protein backbone structure and motion from RDC data J. Magn. Reson. 191 2008 322 334
10. V.B. Chen, W.B. Arendall III, J.J. Headd, D.A. Keedy, R.M. Immormino, G.J. Kapral, L.W. Murray, J.S. Richardson, and D.C. Richardson MolProbity: all-atom structure validation for macromolecular crystallography Acta Crystallogr. D Biol. Crystallogr. 66 2010 12 21
11. G.M. Clore, and C.D. Schwieters How much backbone motion in ubiquitin is required to account for dipolar coupling data measured in multiple alignment media as assessed by independent cross-validation? J. Am. Chem. Soc. 126 2004 2923 2938
12. G.M. Clore, M.A. Robien, and A.M. Gronenborn Exploring the limits of precision and accuracy of protein structures determined by nuclear magnetic resonance spectroscopy J. Mol. Biol. 231 1993 82 102
13. G. Cornilescu, J.L. Marquardt, M. Ottiger, and A. Bax Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase J. Am. Chem. Soc. 120 1998 6836 6837
14. J.F. Doreleijers, A.W. Sousa da Silva, E. Krieger, S.B. Nabuurs, C.A. Spronk, T.J. Stevens, W.F. Vranken, G. Vriend, and G.W. Vuister CING: an integrated residue-based structure validation program suite J. Biomol. NMR 54 2012 267 283
15. A.K. Dunker, I. Silman, V.N. Uversky, and J.L. Sussman Function and structure of inherently disordered proteins Curr. Opin. Struct. Biol. 18 2008 756 764
16. H.J. Dyson, and P.E. Wright Intrinsically unstructured proteins and their functions Nat. Rev. Mol. Cell Biol. 6 2005 197 208
17. S.W. Ginzinger, F. Gerick, M. Coles, and V. Heun CheckShift: automatic correction of inconsistent chemical shift referencing J. Biomol. NMR 39 2007 223 227
18. S. Gore, S. Velankar, and G.J. Kleywegt Implementing an X-ray validation pipeline for the Protein Data Bank Acta Crystallogr. D Biol. Crystallogr. 68 2012 478 483
19. A. Grishaev, J. Wu, J. Trewhella, and A. Bax Refinement of multidomain protein structures by combination of solution small-angle X-ray scattering and NMR data J. Am. Chem. Soc. 127 2005 16621 16628
20. B. Han, Y. Liu, S.W. Ginzinger, and D.S. Wishart SHIFTX2: significantly improved protein chemical shift prediction J. Biomol. NMR 50 2011 43 57
21. R. Henderson, A. Sali, M.L. Baker, B. Carragher, B. Devkota, K.H. Downing, E.H. Egelman, Z. Feng, J. Frank, and N. Grigorieff Outcome of the first Electron Microscopy Validation Task Force meeting Structure 20 2012 205 214
22. Y.J. Huang, R. Powers, and G.T. Montelione Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics J. Am. Chem. Soc. 127 2005 1665 1674
23. Y.J. Huang, A. Rosato, G. Singh, and G.T. Montelione RPF: a quality assessment tool for protein NMR structures Nucleic Acids Res. 40 2012 W542 W546
24. S.G. Hyberts, M.S. Goldberg, T.F. Havel, and G. Wagner The solution structure of eglin c based on measurements of many NOEs and coupling constants and its comparison with X-ray structures Protein Sci. 1 1992 736 751
25. L.A. Kelley, S.P. Gardner, and M.J. Sutcliffe An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies Protein Eng. 9 1996 1063 1065
26. L.A. Kelley, S.P. Gardner, and M.J. Sutcliffe An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures Protein Eng. 10 1997 737 741
27. D.K. Kirchner, and P. Güntert Objective identification of residue ranges for the superposition of protein structures BMC Bioinformatics 12 2011 170
28. O.F. Lange, P. Rossi, N.G. Sgourakis, Y. Song, H.W. Lee, J.M. Aramini, A. Ertekin, R. Xiao, T.B. Acton, G.T. Montelione, and D. Baker Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples Proc. Natl. Acad. Sci. USA 109 2012 10873 10878
29. R.A. Laskowski, J.A. Rullmannn, M.W. MacArthur, R. Kaptein, and J.M. Thornton AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR J. Biomol. NMR 8 1996 477 486
30. K. Lindorff-Larsen, R.B. Best, M.A. Depristo, C.M. Dobson, and M. Vendruscolo Simultaneous determination of protein structure and dynamics Nature 433 2005 128 132
31. B. Mao, R. Guan, and G.T. Montelione Improved technologies now routinely provide protein NMR structures useful for molecular replacement Structure 19 2011 757 766
32. J.L. Markley, A. Bax, Y. Arata, C.W. Hilbers, R. Kaptein, B.D. Sykes, P.E. Wright, and K. Wüthrich Recommendations for the presentation of NMR structures of proteins and nucleic acids Pure Appl. Chem. 70 1998 117 142
33. H.N. Moseley, G. Sahota, and G.T. Montelione Assignment validation software suite for the evaluation and presentation of protein resonance assignment data J. Biomol. NMR 28 2004 341 355
34. S.B. Nabuurs, C.A. Spronk, E. Krieger, H. Maassen, G. Vriend, and G.W. Vuister Quantitative evaluation of experimental NMR restraints J. Am. Chem. Soc. 125 2003 12026 12034
35. M. Nilges Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities J. Mol. Biol. 245 1995 645 660
36. S. Raman, O.F. Lange, P. Rossi, M. Tyka, X. Wang, J. Aramini, G. Liu, T.A. Ramelot, A. Eletsky, and T. Szyperski NMR structure determination for larger proteins using backbone-only data Science 327 2010 1014 1018
37. R.J. Read, P.D. Adams, W.B. Arendall III, A.T. Brunger, P. Emsley, R.P. Joosten, G.J. Kleywegt, E.B. Krissinel, T. Lütteke, and Z. Otwinowski A new generation of crystallographic validation tools for the Protein Data Bank Structure 19 2011 1395 1412
38. W. Rieping, and W.F. Vranken Validation of archived chemical shifts through atomic coordinates Proteins 78 2010 2482 2489
39. A. Rosato, J.M. Aramini, C. Arrowsmith, A. Bagaria, D. Baker, A. Cavalli, J.F. Doreleijers, A. Eletsky, A. Giachetti, and P. Guerry Blind testing of routine, fully automated determination of protein structures from NMR data Structure 20 2012 227 236
40. P. Serrano, B. Pedrini, B. Mohanty, M. Geralt, T. Herrmann, and K. Wüthrich The J-UNIO protocol for automated protein structure determination by NMR in solution J. Biomol. NMR 53 2012 341 354
41. W. Sheffler, and D. Baker RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation Protein Sci. 18 2009 229 239
42. Y. Shen, and A. Bax SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network J. Biomol. NMR 48 2010 13 22
43. D.A. Snyder, and G.T. Montelione Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles Proteins 59 2005 673 686
44. D.A. Snyder, A. Bhattacharya, Y.J. Huang, and G.T. Montelione Assessing precision and accuracy of protein structures derived from NMR data Proteins 59 2005 655 661
45. C.A. Spronk, S.B. Nabuurs, A.M. Bonvin, E. Krieger, G.W. Vuister, and G. Vriend The precision of NMR structure ensembles revisited J. Biomol. NMR 25 2003 225 234
46. A. Struyf, M. Hubert, and P. Rousseeuw Clustering in an object-oriented environment J. Stat. Softw. 1 1997 1 30
47. R. Tejero, D. Snyder, B. Mao, J.M. Aramini, and G.T. Montelione PDBStat: a universal restraint converter and restraint analysis software package for protein NMR J. Biomol. NMR 2013 10.1007/s10858-013-9753-7 Published online July 30, 2013
48. D.L. Theobald, and D.S. Wuttke THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures Bioinformatics 22 2006 2171 2172
49. D.L. Theobald, and D.S. Wuttke Accurate structural correlations from maximum likelihood superpositions PLoS Comput. Biol. 4 2008 e43
50. J. Trewhella, W.A. Hendrickson, G.J. Kleywegt, A. Sali, M. Sato, T. Schwede, D.I. Svergun, J.A. Tainer, J. Westbrook, and H.M. Berman Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB Structure 21 2013 875 881
51. E.L. Ulrich, H. Akutsu, J.F. Doreleijers, Y. Harano, Y.E. Ioannidis, J. Lin, M. Livny, S. Mading, D. Maziuk, and Z. Miller BioMagResBank Nucleic Acids Res. 36 2008 D402 D408
52. H. Valafar, and J.H. Prestegard REDCAT: a residual dipolar coupling analysis tool J. Magn. Reson. 167 2004 228 241
53. G. Vriend WHAT IF: a molecular modeling and drug design program J. Mol. Graph. 8 1990 52 56 29
54. G.W. Vuister, R.H. Fogh, P.M. Hendrickx, J.F. Doreleijers, and A. Gutmanas An overview of tools for the validation of protein NMR structures J. Biomol. NMR 2013 10.1007/s10858-013-9750-x Published online July 23, 2013
55. 13C secondary chemical shifts and its application to nitrogen chemical shift re-referencing J. Biomol. NMR 44 2009 95 99
56. L. Wang, H.R. Eghbalnia, A. Bahrami, and J.L. Markley Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications J. Biomol. NMR 32 2005 13 22
57. B. Wang, Y. Wang, and D.S. Wishart A probabilistic approach for validating protein NMR chemical shift assignments J. Biomol. NMR 47 2010 85 99