Detection of unrealistic molecular environments in protein structures based on expected electron densities

Journal of Biomolecular NMR

Volumn 47, Issue 1, 2010, Pages 33-40

  Ginzinger, Simon W ^a   Weichenberger, Christian X ^a   Sippl, Manfred J ^a  

^a UNIVERSITY OF SALZBURG   (Austria)

Author keywords

Electron density; Error detection; Protein structure

Indexed keywords

ANALYTICAL ERROR; ARTICLE; CHEMICAL ENVIRONMENT; CONTROLLED STUDY; ELECTRON; INSTRUMENT VALIDATION; INTERMETHOD COMPARISON; MOLECULAR DYNAMICS; MOLECULAR MODEL; MOLECULAR WEIGHT; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN INTERACTION; PROTEIN STRUCTURE; QUALITY CONTROL; RELIABILITY; STEREOCHEMISTRY; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; X RAY;

CRYSTALLOGRAPHY, X-RAY; DATABASES, FACTUAL; ELECTRONS; MODELS, CHEMICAL; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEINS; SOFTWARE;

EID: 77951666684     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-010-9408-x     Document Type: Article

References (25)

1. 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 1 235 242 10.1093/nar/28.1.235 (Pubitemid 30047768)
2. CI Branden TA Jones 1990 Between objectivity and subjectivity Nature 343 687 689 10.1038/343687a0 1990Natur.343..687B
3. AT Brünger 1992 Free R value: a novel statistical quantity for assessing the accuracy of crystal structures Nature 355 6359 472 475 10.1038/355472a0 1992Natur.355..472B
4. Brown EN, Ramaswamy S (2007) Quality of protein crystal structures. Acta Crystallogr D Biol Crystallogr 63(Pt 9):941-950. doi: 10.1107/S0907444907033847 (Pubitemid 47346819)
5. C Colovos TO Yeates 1993 Verification of protein structures: patterns of nonbonded atomic interactions Protein Sci 2 1511 1519 10.1002/pro.5560020916
6. Cromer DT, Waber JT (1974) International tables for X-ray crystallography, Vol. IV, Table 2.2 B. Kynoch Press, Birmingham (Present distributor Kluwer Academic Publishers, Dordrecht), pp 99-101
7. Davis I, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB, Snoeyink J, Richardson JS, Richardson DC (2007) Molprobity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35(Web Server issue):W375-W383. doi: 10.1093/nar/gkm216
8. DeLano W (2002) The PyMOL user's manual. DeLano Scientific, Palo Alto
9. Emsley P, Cowtan K (2004) COOT: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60(Pt 12 Pt 1):2126-2132. doi: 10.1107/S0907444904019158 (Pubitemid 41742764)
10. Hooft RW, Vriend G, Sander C, Abola EE (1996) Errors in protein structures. Nature 381(6580):272. doi: 10.1038/381272a0
11. RP Joosten J Salzemann V Bloch H Stockinger AC Berglund C Blanchet E Bongcam-Rudloff C Combet AL Da Costa G Deleage M Diarena R Fabbretti G Fettahi V Flegel A Gisel V Kasam T Kervinen E Korpelainen K Mattila M Pagni M Reichstadt V Breton IJ Tickle V G 2009 PDB-REDO: automated re-refinement of X-ray structure models in the pdb J Appl Crystallogr 42 376 384 10.1107/S0021889809008784
12. Joosten RP, Womack T, Vriend G, Bricogne G (2009b) Re-refinement from deposited X-ray data can deliver improved models for most PDB entries. Acta Crystallogr D Biol Crystallogr 65(Pt 2):176-185. doi: 7591
13. Kleywegt GJ (2009) On vital aid: the why, what and how of validation. Acta Crystallogr D Biol Crystallogr 65(Pt 2):134-139. doi: 10.1107/ S090744490900081X
14. Kleywegt GJ, Harris MR, Zou JY, Taylor TC, Wählby A, Jones TA (2004) The uppsala electron-density server. Acta Crystallogr D Biol Crystallogr 60(Pt 12 Pt 1):2240-2249. doi: 1107/S0907444904013253
15. Lüthy R, Bowie JU, Eisenberg D (1992) Assessment of protein models with three-dimensional profiles. Nature 356(6364):83-85. doi: 10.1038/356083a0
16. Melo F, Feytmans E (1998) Assessing protein structures with a non-local atomic interaction energy. J Mol Biol 277(5):1141-1152. doi: 10.1006/jmbi.1998.1665 (Pubitemid 28190852)
17. Read RJ, Kleywegt GJ (2009) Case-controlled structure validation. Acta Crystallogr D Biol Crystallogr 65(Pt 2):140-147. doi: 10.1107/S0907444908041085
18. Saccenti E, Rosato A (2008) The war of tools: how can NMR spectroscopists detect errors in their structures? J Biomol NMR 40(4):251-261. doi: 10.1007/s10858-008-9228-4
19. Sippl MJ (1993) Recognition of errors in three-dimensional structures of proteins. Proteins 17(4):355-362. doi: 10.1002/prot.340170404 (Pubitemid 23358545)
20. Sippl MJ, Wiederstein M (2008) A note on difficult structure alignment problems. Bioinformatics 24(3):426-427. doi: 10.1093/bioinformatics/btm622 (Pubitemid 351189021)
21. Suhrer S, Wiederstein M, Gruber M, Sippl MJ (2009) COPS-a novel workbench for explorations in fold space. Nucleic Acids Res 37:W539-W544. doi: 10.1093/nar/gkp411
22. Tronrud DE, Matthews BW (2009) Sorting the chaff from the wheat at the PDB. Protein Sci 18(1):2-5. doi: 10.1002/pro.13
23. G Vriend C Sander 1993 Quality control of protein models: directional atomic contact analysis J Appl Cryst 26 47 60 10.1107/S0021889892008240 (Pubitemid 23611937)
24. Weichenberger CX, Sippl MJ (2006) Self-consistent assignment of asparagine and glutamine amide rotamers in protein crystal structures. Structure 14(6):967-972. doi: 10.1016/j.str.2006.04.002 (Pubitemid 43831657)
25. Word JM, Lovell SC, Richardson JS, Richardson DC (1999) Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 285(4):1735-1747. doi: 10.1006/jmbi.1998.2401 (Pubitemid 29060467)