Related ArticlesApplication of 1H NMR chemical shifts to measure the quality of protein structures.
J Mol Biol. 1995 Apr 7;247(4):541-6
Authors: Williamson MP, Kikuchi J, Asakura T
We have developed a program that can calculate proton NMR chemical shifts for proteins, using a set of co-ordinates provided for example from an X-ray or NMR structure. When applied to NMR structures, agreement between calculated and observed shifts is generally of the same quality as that for crystal structures of resolution between 2.0 and 3.0 A. There is a rather weak correlation between standard deviation (SD) and the number of NMR constraints per residue, but none with the root-mean-square deviation of one NMR structure from another. Where minimised averaged structures are present, they have about the same SD as the population from which they were taken. Refinement methods such as energy minimisation and the use of relaxation matrices and back calculation produce little or no improvement in SD. The calculation has several applications, particularly as an independent means of measuring the quality of a structure (either in the crystal or in solution), and in identifying possible assignment errors.
Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids
Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids
Abstract Unravelling the complex correlation between chemical shifts of 13 C α, 13 C β, 13 C�, 1 H α, 15 N, 1 H N atoms in amino acids of proteins from NMR experiment and local structural environments of amino acids facilitates the assignment of secondary structures of proteins. This is an important impetus for both determining the three-dimensional structure and understanding the biological function of proteins. The previous...
nmrlearner
Journal club
0
11-14-2011 08:45 AM
Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings.
Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings.
Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings.
J Am Chem Soc. 2011 Apr 5;
Authors: Sgourakis NG, Lange OF, Dimaio F, Andre? I, Fitzkee NC, Rossi P, Montelione GT, Bax A, Baker D
Symmetric protein dimers, trimers, and higher-order cyclic oligomers play key roles in many biological processes. However, structural studies of oligomeric systems by solution NMR...
nmrlearner
Journal club
0
04-07-2011 09:54 PM
Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings
Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings
Nikolaos G. Sgourakis, Oliver F. Lange, Frank DiMaio, Ingemar Andre?, Nicholas C. Fitzkee, Paolo Rossi, Gaetano T. Montelione, Ad Bax and David Baker
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja111318m/aop/images/medium/ja-2010-11318m_0008.gif
Journal of the American Chemical Society
DOI: 10.1021/ja111318m
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...
nmrlearner
Journal club
0
04-06-2011 10:54 AM
[NMR paper] High-quality homology models derived from NMR and X-ray structures of E. coli protein
High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases.
Related Articles High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases.
Protein Sci. 2005 Jun;14(6):1597-608
Authors: Liu G, Li Z, Chiang Y, Acton T, Montelione GT, Murray D, Szyperski T
The structural...
nmrlearner
Journal club
0
11-25-2010 08:21 PM
[NMR paper] Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality a
Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.
Related Articles Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.
J Am Chem Soc. 2005 Feb 16;127(6):1665-74
Authors: Huang YJ, Powers R, Montelione GT
One of the most important challenges in modern protein NMR is the development of fast and sensitive structure quality assessment measures that can be...
nmrlearner
Journal club
0
11-24-2010 11:14 PM
[NMR paper] Improving the quality of protein structures derived by NMR spectroscopy.
Improving the quality of protein structures derived by NMR spectroscopy.
Related Articles Improving the quality of protein structures derived by NMR spectroscopy.
J Biomol NMR. 2002 Mar;22(3):281-9
Authors: Spronk CA, Linge JP, Hilbers CW, Vuister GW
Biomolecular structures provide the basis for many studies in several research areas such as homology modelling, structure-based drug design and functional genomics. It is an important prerequisite that the structure is reliable in terms of accurate description of the experimental data, and in...
nmrlearner
Journal club
0
11-24-2010 08:49 PM
[NMR paper] Improving the quality of NMR and crystallographic protein structures by means of a co
Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases.
...
nmrlearner
Journal club
0
08-22-2010 02:27 PM
[NMR paper] AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved
AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.
Related Articles AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.
J Biomol NMR. 1996 Dec;8(4):477-86
Authors: Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM
The AQUA and PROCHECK-NMR programs provide a means of validating the geometry and restraint violations of an ensemble of protein structures solved by solution NMR. The outputs include a detailed breakdown of the restraint violations, a...
Application of 1H NMR chemical shifts to measure the quality of protein structures.
Linear Mode
