RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank

Proteins: Structure, Function and Genetics

Volumn 59, Issue 4, 2005, Pages 662-672

  Nederveen, Aart J ^a   Doreleijers, Jurgen F ^b   Vranken, Wim ^c   Miller, Zachary ^d   Spronk, Chris A E M ^e   Nabuurs, Sander B ^e   Güntert, Peter ^f   Livny, Miron ^d   Markley, John L ^b   Nilges, Michael ^g   Ulrich, Eldon L ^b   Kaptein, Robert ^a   Bonvin, Alexandre M J J ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^d University of Wisconsin   (United States)

^e RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

^f RIKEN YOKOHAMA INSTITUTE   (Japan)

^g INSTITUT PASTEUR   (France)

Author keywords

Experimental restraints; NMR; Structure calculation; Structure refinement; Structure validation; Water refinement

Indexed keywords

PROTEIN;

ARTICLE; CALCULATION; COMPUTER PROGRAM; CORRELATION ANALYSIS; DATA BASE; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN STRUCTURE; STATISTICAL MODEL; STRUCTURE ANALYSIS; VALIDATION PROCESS;

DATABASES, PROTEIN; PROTEIN CONFORMATION; PROTEINS; REPRODUCIBILITY OF RESULTS; STRESS, MECHANICAL;

EID: 21044449889     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20408     Document Type: Article

References (34)

1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
2. Laskowski RA. Structural quality assurance. Methods Biochem Anal 2003;44:273-303.
3. Wüthrich K. NMR of Proteins and Nucleic Acids. New York: John Wiley & Sons; 1986.
4. Güntert P. Structure calculation of biological macromolecules from NMR data. Q Rev Biophys 1998;31:145-237.
5. Havel TF. An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance. Prog Biophys Mol Biol 1991;56:43-78.
6. Braun W, Go N. Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm. J Mol Biol 1985;186:611-626.
7. Kaptein R, Zuiderweg ER, Scheek RM, Boelens R, van Gunsteren WF. A protein structure from nuclear magnetic resonance data. lac repressor headpiece. J Mol Biol 1985;182:179-182.
8. Brünger AT. X-PLOR Manual (Version 4.0). Department of Molecular Biophysics and Biochemistry: Yale University; 1996.
9. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 1998;54:905-921.
10. Güntert P, Mumenthaler C, Wüthrich K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 1997;273:283-298.
11. Doreleijers JF, Raves ML, Rullmann T, Kaptein R. Completeness of NOEs in protein structure: a statistical analysis of NMR. J Biomol NMR 1999;14:123-132.
12. Nabuurs SB, Spronk CAEM, Vriend G, Vuister GW. Concepts and tools for NMR restraint analysis and validation. Concepts in Magnetic Resonance 2004;22A:90-105.
13. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 1993;26:283-291.
14. Hooft RW, Vriend G, Sander C, Abola EE. Errors in protein structures. Nature 1996;381:272.
15. Doreleijers JF, Rullmann JA, Kaptein R. Quality assessment of NMR structures: a statistical survey. J Mol Biol 1998;281:149-164.
16. Spronk CA, Linge JP, Hilbers CW, Vuister GW. Improving the quality of protein structures derived by NMR spectroscopy. J Biomol NMR 2002;22:281-289.
17. Linge JP, Williams MA, Spronk CA, Bonvin AM, Nilges M. Refinement of protein structures in explicit solvent. Proteins 2003;50:496-506.
18. Nabuurs SB, Nederveen AJ, Vranken W, Doreleijers JF, Bonvin AMJJ, Vuister GW, Vriend G, Spronk CAEM. DRESS: a database of REfined solution NMR structures. Proteins 2004;55:483-486.
19. Doreleijers JF, Mading S, Maziuk D, Sojourner K, Yin L, Zhu J, Markley JL, Ulrich EL. BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank. J Biomol NMR 2003;26:139-146.
20. Doreleijers JF, Nederveen AJ, Vranken W, Lin J, Bonvin AMJJ, Kaptein R, Markley JL, Ulrich EL. BioMagResBank databases DOCR and FRED with converted and filtered sets of experimental NMR constraints and coordinates from over 500 protein PDB structures. J Biomol NMR 2004, in press.
21. Engh RA, Huber R. Accurate bond and angle parameters for X-ray proteinstructure refinement. Acta Crystallogr A 1991;47:392-400.
22. http://www.accelrys.com/insight/discover.html.
23. Markley JL, Bax A, Arata Y, Hilbers CW, Kaptein R, Sykes BD, Wright PE, Wüthrich K. Recommendations for the presentation of NMR structures of proteins and nucleic acids-IUPAC-IUBMB-IUPAB Inter-Union Task Group on the standardization of data bases of protein and nucleic acid structures determined by NMR spectroscopy. Eur J Biochem 1998;256:1-15.
24. Fogh R, Ionides J, Ulrich E, Boucher W, Vranken W, Linge JP, Habeck M, Rieping W, Bhat TN, Westbrook J, Henrick K, Gilliland G, Berman H, Thornton J, Nilges M, Markley J, Laue E. The CCPN project: an interim report on a data model for the NMR community. Nat Struct Biol 2002;9:416-418.
25. 1H-NMR. Proteins 1993;17:297-309.
26. Güntert, P. Automated NMR protein structure calculation. Prog NMR Spectrosc 2003;43:105-125.
27. Linge JP, Habeck M, Rieping W, Nilges M. ARIA: automated NOE assignment and NMR structure calculation. Bioinformatics 2003; 19:315-316.
28. Litzkow M, Livny M, Mutka M. Condor - a hunter of idle workstations. In: Proceedings of the 8th international conference of distributed computing systems, 1988.
29. Thain D, Tannenbaum T, Livny M. Condor and the grid. In: Herman F, Fox G, Hey T, editors. Grid computing: making the global infrastructure a reality. New York: John Wiley & Sons Inc; 2002; p 299-335.
30. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
31. Nabuurs SB, Spronk CA, Krieger E, Maassen H, Vriend G, Vuister GW. Quantitative evaluation of experimental NMR-restraints. J Am Chem Soc 2003;125:12026-12034.
32. Nilges M, Clore M, Gronenborn AM. A simple method for delineating well defined and variable regions in protein structures determined from interproton distance data. FEBS Lett 1987;219:11-16.
33. Spronk CA, Nabuurs SB, Bonvin AM, Krieger E, Vuister GW, Vriend G. The precision of NMR structure ensembles revisited. J Biomol NMR 2003;25:225-234.
34. Rice LM, Brunger AT. Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Proteins 1994;19:277-290.