Related ArticlesProtein NMR Structures Refined without NOE Data.
PLoS One. 2014;9(10):e108888
Authors: Ryu H, Kim TR, Ahn S, Ji S, Lee J
Abstract
The refinement of low-quality structures is an important challenge in protein structure prediction. Many studies have been conducted on protein structure refinement; the refinement of structures derived from NMR spectroscopy has been especially intensively studied. In this study, we generated flat-bottom distance potential instead of NOE data because NOE data have ambiguity and uncertainty. The potential was derived from distance information from given structures and prevented structural dislocation during the refinement process. A simulated annealing protocol was used to minimize the potential energy of the structure. The protocol was tested on 134 NMR structures in the Protein Data Bank (PDB) that also have X-ray structures. Among them, 50 structures were used as a training set to find the optimal "width" parameter in the flat-bottom distance potential functions. In the validation set (the other 84 structures), most of the 12 quality assessment scores of the refined structures were significantly improved (total score increased from 1.215 to 2.044). Moreover, the secondary structure similarity of the refined structure was improved over that of the original structure. Finally, we demonstrate that the combination of two energy potentials, statistical torsion angle potential (STAP) and the flat-bottom distance potential, can drive the refinement of NMR structures.
PMID: 25279564 [PubMed - as supplied by publisher]
ProteinNMR Structures Refined with Rosetta Have HigherAccuracy Relative to Corresponding X-ray Crystal Structures
ProteinNMR Structures Refined with Rosetta Have HigherAccuracy Relative to Corresponding X-ray Crystal Structures
Binchen Mao, Roberto Tejero, David Baker and Gaetano T. Montelione
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja409845w/aop/images/medium/ja-2013-09845w_0009.gif
Journal of the American Chemical Society
DOI: 10.1021/ja409845w
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/7Lshnyi2_Vs
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01-24-2014 10:47 AM
[NMR paper] Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures.
Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures.
Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures.
J Am Chem Soc. 2014 Jan 6;
Authors: Mao B, Tejero R, Baker D, Montelione GT
Abstract
We have found that refinement of protein NMR structures using Rosetta with experimental NMR restraints yields more accurate protein NMR structures than those that have been deposited in the PDB using standard refinement...
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01-08-2014 11:23 AM
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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02-05-2011 05:28 PM
[NMR paper] Assessing precision and accuracy of protein structures derived from NMR data.
Assessing precision and accuracy of protein structures derived from NMR data.
Related Articles Assessing precision and accuracy of protein structures derived from NMR data.
Proteins. 2005 Jun 1;59(4):655-61
Authors: Snyder DA, Bhattacharya A, Huang YJ, Montelione GT
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11-25-2010 08:21 PM
[NMR paper] Calculating protein structures from NMR data.
Calculating protein structures from NMR data.
Related Articles Calculating protein structures from NMR data.
Methods Mol Biol. 1997;60:157-94
Authors: Güntert P
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08-22-2010 03:31 PM
[NMR paper] Calculating protein structures from NMR data.
Calculating protein structures from NMR data.
Related Articles Calculating protein structures from NMR data.
Methods Mol Biol. 1997;60:157-94
Authors: Güntert P
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08-22-2010 03:03 PM
[NMR paper] Conformational analysis of protein structures derived from NMR data.
Conformational analysis of protein structures derived from NMR data.
Related Articles Conformational analysis of protein structures derived from NMR data.
Proteins. 1993 Nov;17(3):232-51
Authors: MacArthur MW, Thornton JM
A study is presented of the conformational characteristics of NMR-derived protein structures in the Protein Data Bank compared to X-ray structures. Both ensemble and energy-minimized average structures are analyzed. We have addressed the problem using the methods developed for crystal structures by examining the distribution...
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[NMR paper] Computational methods for determining protein structures from NMR data.
Computational methods for determining protein structures from NMR data.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Computational methods for determining protein structures from NMR data.
Biochem Pharmacol. 1990 Jul 1;40(1):15-22
Authors: Gippert GP, Yip PF, Wright PE, Case DA
The general procedures by which solution structures of proteins may be deduced from distance and angular constraints derived from NMR are reviewed, with an emphasis on practical aspects of...
Protein NMR Structures Refined without NOE Data.
Linear Mode
