Related ArticlesA systematic comparison of three structure determination methods from NMR data: dependence upon quality and quantity of data.
J Biomol NMR. 1992 Jul;2(4):373-88
Authors: Liu Y, Zhao D, Altman R, Jardetzky O
We have systematically examined how the quality of NMR protein structures depends on (1) the number of NOE distance constraints, (2) their assumed precision, (3) the method of structure calculation and (4) the size of the protein. The test sets of distance constraints have been derived from the crystal structures of crambin (5 kDa) and staphylococcal nuclease (17 kDa). Three methods of structure calculation have been compared: Distance Geometry (DGEOM), Restrained Molecular Dynamics (XPLOR) and the Double Iterated Kalman Filter (DIKF). All three methods can reproduce the general features of the starting structure under all conditions tested. In many instances the apparent precision of the calculated structure (as measured by the RMS dispersion from the average) is greater than its accuracy (as measured by the RMS deviation of the average structure from the starting crystal structure). The global RMS deviations from the reference structures decrease exponentially as the number of constraints is increased, and after using about 30% of all potential constraints, the errors asymptotically approach a limiting value. Increasing the assumed precision of the constraints has the same qualitative effect as increasing the number of constraints. For comparable numbers of constraints/residue, the precision of the calculated structure is less for the larger than for the smaller protein, regardless of the method of calculation. The accuracy of the average structure calculated by Restrained Molecular Dynamics is greater than that of structures obtained by purely geometric methods (DGEOM and DIKF).
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
Open Biochem J. 2010;4:83-95
Authors: Sikic K, Tomic S, Carugo O
Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in...
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[NMR paper] Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures?
Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures?
Related Articles Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures?
Proteins. 2005 Jul 1;60(1):139-47
Authors: Garbuzynskiy SO, Melnik BS, Lobanov MY, Finkelstein AV, Galzitskaya OV
We have compared structures of 78 proteins determined by both NMR and X-ray methods. It is shown that X-ray and NMR structures...
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12-01-2010 06:56 PM
[NMR paper] Multidimensional NMR methods for protein structure determination.
Multidimensional NMR methods for protein structure determination.
Related Articles Multidimensional NMR methods for protein structure determination.
IUBMB Life. 2001 Dec;52(6):291-302
Authors: Kanelis V, Forman-Kay JD, Kay LE
Structural studies of proteins are critical for understanding biological processes at the molecular level. Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for obtaining structural and dynamic information on proteins and protein-ligand complexes. In the present review, methodologies for NMR structure...
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[NMR paper] Expression and secondary structure determination by NMR methods of the major house du
Expression and secondary structure determination by NMR methods of the major house dust mite allergen Der p 2.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-standard-jbc_full_free.gif Related Articles Expression and secondary structure determination by NMR methods of the major house dust mite allergen Der p 2.
J Biol Chem. 1997 Oct 24;272(43):26893-8
Authors: Mueller GA, Smith AM, Williams DC, Hakkaart GA, Aalberse RC, Chapman MD, Rule GS, Benjamin DC
There exists a strong...
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08-22-2010 05:08 PM
Combining NMR and EPR Methods for Homodimer Protein Structure Determination.
Combining NMR and EPR Methods for Homodimer Protein Structure Determination.
Related Articles Combining NMR and EPR Methods for Homodimer Protein Structure Determination.
J Am Chem Soc. 2010 Aug 10;
Authors: Yang Y, Ramelot TA, McCarrick RM, Ni S, Feldmann EA, Cort JR, Wang H, Ciccosanti C, Jiang M, Janjua H, Acton TB, Xiao R, Everett JK, Montelione GT, Kennedy MA
There is a general need to develop more powerful and more robust methods for structural characterization of homodimers, homo-oligomers, and multiprotein complexes using...
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08-17-2010 03:36 AM
Structure-oriented methods for protein NMR data analysis
Structure-oriented methods for protein NMR data analysis
Publication year: 2010
Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 3 March 2010</br>
Guillermo A., Bermejo , Miguel, Llinás</br>
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Combining NMR and EPR Methods for Homodimer Protein Structure Determination
http://pubs.acs.org//appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja105080h/aop/images/medium/ja-2010-05080h_0003.gif
Combining NMR and EPR Methods for Homodimer Protein Structure Determination
There is a general need to develop more powerful and more robust methods for structural characterization of homodimers, homo-oligomers, and multiprotein complexes using solution-state NMR methods. In recent years, there has been increasing emphasis on integrating distinct and complementary methodologies for structure determination of multiprotein ...
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08-14-2010 05:56 AM
KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies
KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies
Naohiro Kobayashi, Junji Iwahara, Seizo Koshiba, Tadashi Tomizawa, Naoya Tochio, Peter Güntert, Takanori Kigawa and Shigeyuki Yokoyama
Journal of Biomolecular NMR; 2007; 39(1) pp 31 - 52
Abstract:
The recent expansion of structural genomics has increased the demands for quick and accurate protein structure determination by NMR spectroscopy. The conventional strategy without an automated protocol can no longer satisfy the needs of high-throughput...
A systematic comparison of three structure determination methods from NMR data: depen
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