Estimating structure quality trends in the Protein Data Bank by equivalent resolution

Computational Biology and Chemistry

Volumn 46, Issue , 2013, Pages 8-15

  Bagaria, Anurag ^a   Jaravine, Victor ^a   Güntert, Peter ^a  

^a GOETHE UNIVERSITY   (Germany)

Author keywords

Equivalent resolution; Multiple linear regression; PDB; Protein structure validation; Structure quality; X ray and NMR

Indexed keywords

AB INITIO CALCULATIONS; COMPUTATIONAL TECHNIQUE; EXPERIMENTAL TECHNIQUES; MULTIPLE LINEAR REGRESSIONS; PDB; PROTEIN STRUCTURES; STRUCTURE DETERMINATION; STRUCTURE QUALITY;

DATABASE SYSTEMS; LINEAR REGRESSION;

PROTEINS;

PHORBOL DIBUTYRATE; PROTEIN;

ARTICLE; CHEMISTRY; EQUIVALENT RESOLUTION; IMAGE PROCESSING; MULTIPLE LINEAR REGRESSION ANALYSIS; MULTIVARIATE ANALYSIS; PROTEIN DATABASE; PROTEIN STRUCTURE VALIDATION; STANDARD; STATISTICS; STRUCTURE QUALITY; X-RAY AND NMR;

EQUIVALENT RESOLUTION; MULTIPLE LINEAR REGRESSION; PDB; PROTEIN STRUCTURE VALIDATION; STRUCTURE QUALITY; X-RAY AND NMR;

DATABASES, PROTEIN; IMAGE PROCESSING, COMPUTER-ASSISTED; MULTIVARIATE ANALYSIS; PROTEINS;

EID: 84879098708     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2013.04.004     Document Type: Article

References (39)

1. A. Bagaria, V. Jaravine, Y.P.J. Huang, G.T. Montelione, and P. Güntert Protein structure validation by generalized linear model root-mean-square deviation prediction Protein Science 21 2012 229 238
2. M. Berjanskii, J. Zhou, Y. Liang, G. Lin, and D.S. Wishart Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures Journal of Biomolecular NMR 53 2012 167 180
3. A. Bhattacharya, R. Tejero, and G.T. Montelione Evaluating protein structures determined by structural genomics consortia Proteins: Structure, Function, and Bioinformatics 66 2007 778 795
4. V.B. Chen, W.B. Arendall, J.J. Headd, D.A. Keedy, and R.M. Immormino MolProbity: all-atom structure validation for macromolecular crystallography Acta Crystallographica Section D: Biological Crystallography 66 2010 12 21
5. H.Y. Chen, M.M. Rogalski, and J.N. Anker Advances in functional X-ray imaging techniques and contrast agents Physical Chemistry Chemical Physics 14 2012 13469 13486
6. S. Cristobal, A. Zemla, D. Fischer, L. Rychlewski, and A. Elofsson A study of quality measures for protein threading models BMC Bioinformatics 2 2001, Article No.: 5
7. I.W. Davis, L.W. Murray, J.S. Richardson, and D.C. Richardson MolProbity: structure validation and all-atom contact analysis for nucleic acids and their complexes Nucleic Acids Research 32 2004 W615 W619
8. I.W. Davis, A. Leaver-Fay, V.B. Chen, J.N. Block, and G.J. Kapral MolProbity: all-atom contacts and structure validation for proteins and nucleic acids Nucleic Acids Research 35 2007 W375 W383
9. F. DiMaio, T.C. Terwilliger, R.J. Read, A. Wlodawer, and G. Oberdorfer Improved molecular replacement by density- and energy-guided protein structure optimization Nature 473 2011 540-U149
10. J.F. Doreleijers, A.W. Sousa da Silva, E. Krieger, S.B. Nabuurs, and C.A.E.M. Spronk CING: an integrated residue-based structure validation program suite Journal of Biomolecular NMR 54 2012 267 283
11. D. Eisenberg, R. Lüthy, and J.U. Bowie VERIFY3D: assessment of protein models with three-dimensional profiles Methods in Enzymology 277 1997 396 404
12. C.A. Floudas, H.K. Fung, S.R. McAllister, M. Mönnigmann, and R. Rajgaria Advances in protein structure prediction and de novo protein design: a review Chemical Engineering Science 61 2006 966 988 (Pubitemid 41655853)
13. P. Güntert Automated structure determination from NMR spectra European Biophysics Journal 38 2009 129 143
14. J.M. Holton, and K.A. Frankel The minimum crystal size needed for a complete diffraction data set Acta Crystallographica Section D: Biological Crystallography 66 2010 393 408
15. R.W.W. Hooft, G. Vriend, C. Sander, and E.E. Abola Errors in protein structures Nature 381 1996 272
16. 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 Journal of the American Chemical Society 127 2005 1665 1674 (Pubitemid 40229151)
17. Y.J. Huang, A. Rosato, G. Singh, and G.T. Montelione RPF: a quality assessment tool for protein NMR structures Nucleic Acids Research 40 2012 W542 W546
18. J. Janin, K. Henrick, J. Moult, L. Ten Eyck, and M.J.E. Sternberg CAPRI: a critical assessment of predicted interactions Proteins-Structure Function and Bioinformatics 52 2003 2 9 (Pubitemid 36648842)
19. R.P. Joosten, T. Womack, G. Vriend, and G. Bricogne Re-refinement from deposited X-ray data can deliver improved models for most PDB entries Acta Crystallographica Section D: Biological Crystallography 65 2009 176 185
20. L.A. Kelley, and M.J.E. Sternberg Protein structure prediction on the Web: a case study using the Phyre server Nature Protocols 4 2009 363 371
21. I.D. Kuntz, G.M. Crippen, P.A. Kollman, and D. Kimelman Calculation of protein tertiary structure Journal of Molecular Biology 106 1976 983 994
22. A.H. Kwan, M. Mobli, P.R. Gooley, G.F. King, and J.P. Mackay Macromolecular NMR spectroscopy for the non-spectroscopist FEBS Journal 278 2011 687 703
23. R.A. Laskowski, M.W. Macarthur, D.S. Moss, and J.M. Thornton PROCHECK: a program to check the stereochemical quality of protein structures Journal of Applied Crystallography 26 1993 283 291
24. R.A. Laskowski, J.A.C. Rullmann, M.W. MacArthur, R. Kaptein, and J.M. Thornton AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR Journal of Biomolecular NMR 8 1996 477 486 (Pubitemid 126706801)
25. S.C. Lovell, I.W. Davis, W.B. Adrendall, P.I.W. de Bakker, and J.M. Word Structure validation by Cα geometry: φ, ψ and Cβ deviation Proteins: Structure, Function, and Genetics 50 2003 437 450
26. D.L. Minor Jr. The neurobiologist's guide to structural biology: a primer on why macromolecular structure matters and how to evaluate structural data Neuron 54 2007 511 533 (Pubitemid 46756138)
27. J. Moult, K. Fidelis, A. Kryshtafovych, B. Rost, and A. Tramontano Critical assessment of methods of protein structure prediction-Round VIII Proteins: Structure, Function, and Bioinformatics 77 2009 1 4
28. I.J. Myung, and M.A. Pitt Applying Occam's razor in modeling cognition: a Bayesian approach Psychonomic Bulletin & Review 4 1997 79 95 (Pubitemid 127461348)
29. R.J. Pantazes, M.J. Grisewood, and C.D. Maranas Recent advances in computational protein design Current Opinion in Structural Biology 21 2011 467 472
30. A. Rosato, A. Bagaria, D. Baker, B. Bardiaux, and A. Cavalli CASD-NMR: critical assessment of automated structure determination by NMR Nature Methods 6 2009 625 626
31. A. Rosato, J.M. Aramini, C. Arrowsmith, A. Bagaria, and D. Baker Blind testing of routine, fully automated determination of protein structures from NMR data Structure 20 2012 227 236
32. R. Sanchez, and A. Sali Advances in comparative protein-structure modelling Current Opinion in Structural Biology 7 1997 206 214 (Pubitemid 27156719)
33. N. Siew, A. Elofsson, L. Rychiewski, and D. Fischer MaxSub: an automated measure for the assessment of protein structure prediction quality Bioinformatics 16 2000 776 785
34. K. Sikic, S. Tomic, and O. Carugo Systematic comparison of crystal and NMR protein structures deposited in the Protein Data Bank Open Biochemestry Journal 4 2010 83 95
35. M.J. Sippl Recognition of errors in 3-dimensional structures of proteins Proteins: Structure, Function, and Genetics 17 1993 355 362 (Pubitemid 23358545)
36. G.M. Tomkins, K.L. Yielding, N. Talal, and J.F. Curran Protein structure and biological regulation Cold Spring Harbor Symposia on Quantitative Biology 28 1963 461 471
37. Vriend G WHAT IF: a molecular modeling and drug design program Journal of Molecular Graphics 8 1990 52 56 (Pubitemid 20717037)
38. B. Wallner, and Elofsson A Can correct protein models be identified? Protein Science 12 2003 1073 1086 (Pubitemid 36505441)
39. A. Wlodawer, W. Minor, Z. Dauter, and Jaskolski M Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures Febs Journal 275 2008 1 21 (Pubitemid 350294067)