The advantages and limitations of protein crystal structures

Trends in Pharmacological Sciences

Volumn 26, Issue 1, 2005, Pages 10-14

  Acharya, K Ravi ^a   Lloyd, Matthew D ^b  

^a University of Bath   (United Kingdom)

^b UNIVERSITY OF BATH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CRYSTAL STRUCTURE; ERROR; MACROMOLECULE; MEDICAL RESEARCH; MOLECULAR MODEL; PRIORITY JOURNAL; QUALITATIVE ANALYSIS; REVIEW; X RAY DIFFRACTION;

EID: 11144243170     PISSN: 01656147     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tips.2004.10.011     Document Type: Article

References (27)

1. G.A. Kleywegt Validation of protein crystal structures Acta Crystallogr. D Biol. Crystallogr. 56 2000 249 265
2. R. Thaimattam, and M. Jaskolski Synchrotron radiation in atomic-resolution studies of protein structure J. Alloys Compounds 362 2004 12 20
3. M.A. DePristo Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography Structure 12 2004 831 838
4. E. Garman Cool data: quality AND quantity Acta Crystallogr D Biol Crystallogr. D55 1999 1641 1653
5. A.T. Brünger Crystallographic refinement by simulated annealing - Application to crambin Acta Crystallogr. A45 1989 50 61
6. A. Hodel Model bias in macromolecular crystal structures Acta Crystallogr. A48 1992 851 858
7. A.T. Brünger Assessment of phase accuracy by cross validation: the free R-value. Methods and applications Acta Crystallogr. D Biol. Crystallogr. 49 1993 24 36
8. A.T. Brünger Free R-Value - A novel statistical quantity for assessing the accuracy of crystal structures Nature 355 1992 472 475
9. G.J. Kleywegt, and A.T. Brünger Checking your imagination: applications of the free R value Structure 4 1996 897 904
10. C.I. Branden, and T.A. Jones Between objectivity and subjectivity Nature 343 1990 687 689
11. G.J. Kleywegt, and T.A. Jones Where freedom is given, liberties are taken Structure 3 1995 535 540
12. E. Dodson The role of validation in macromolecular crystallography Acta Crystallogr D Biol Crystallogr. D54 1998 1109 1118
13. G.J. Swaminathan Crystal structures of oligomeric forms of the IP-10/CXCL10 chemokine Structure 11 2003 521 532
14. G.N. Ramachandran, and V. Sasisekharan Conformation of polypeptides and proteins Adv. Protein Chem. 23 1968 283 438
15. β deviation Proteins 50 2003 437 450
16. R.A. Laskowski Procheck - a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26 1993 283 291
17. J.M. Petock Analysis of protein structures reveals regions of rare backbone conformation at functional sites Proteins 53 2003 872 879
18. L.L. Videau The cis-Pro touch-turn: A rare motif preferred at functional sites Proteins 56 2004 298 309
19. R.A. Laskowski PDBsum: summaries and analyses of PDB structures Nucleic Acids Res. 29 2001 221 222
20. A.A. Vaguine SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model Acta Crystallogr D Biol Crystallogr. D55 1999 191 205
21. I.W. Davis MolProbity: structure validation and all-atom contact analysis for nucleic acids and their complexes Nucleic Acids Res. 32 2004 W615 W619
22. G. Vriend WHAT IF: a molecular modeling and drug design program J. Mol. Graph. 8 1990 52 56
23. J.A. Erickson Lessons in molecular recognition: The effects of ligand and protein flexibility in molecular docking accuracy J. Med. Chem. 47 2004 45 55
24. P. Walian Structural genomics of membrane proteins Gen. Biol. 5 2004 215.211 215.218
25. B. Contreras-Moreira Comparative modelling: an essential methodology for protein structure prediction in the post-genomic era Appl. Bioinformatics 1 2002 177 190
26. C. DeWeese-Scott, and J. Moult Molecular modelling of protein function regions Proteins: Structure, function and bioinformatics 55 2003 942 961
27. W.L. Bragg The structure of crystals as indicated by their diffraction of X-rays Proc. Roy. Soc. A89 1913 248 277