RNAs play myriad functional and regulatory roles in the cell. Despite their significance, three-dimensional structure elucidation of RNA molecules lags significantly behind that of proteins. NMR-based studies are often rate-limited by the assignment of chemical shifts. Automation of the chemical shift assignment process can greatly facilitate structural studies, however, accurate chemical shift predictions rely on a robust and complete chemical shift database for training. We searched the...
[NMR paper] (1)H, (13)C and (15)N NMR chemical shift assignments of A. thaliana RCD1 RST.
(1)H, (13)C and (15)N NMR chemical shift assignments of A. thaliana RCD1 RST.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles (1)H, (13)C and (15)N NMR chemical shift assignments of A. thaliana RCD1 RST.
Biomol NMR Assign. 2017 Jun 07;:
Authors: Tossavainen H, Hellman M, Vainonen JP, Kangasjärvi J, Permi P
Abstract
The A. thaliana RCD1 (radical-induced cell death1) protein is a cellular signaling hub protein which interacts with...
nmrlearner
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06-10-2017 05:21 PM
Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria
Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria
Abstract
We have determined refined multidimensional chemical shift ranges for intra-residue correlations (13Câ??13C, 15Nâ??13C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 13C chemical shifts...
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01-19-2016 07:37 PM
[NMR paper] Probabilistic validation of protein NMR chemical shift assignments.
Probabilistic validation of protein NMR chemical shift assignments.
Probabilistic validation of protein NMR chemical shift assignments.
J Biomol NMR. 2016 Jan 2;
Authors: Dashti H, Tonelli M, Lee W, Westler WM, Cornilescu G, Ulrich EL, Markley JL
Abstract
Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments....
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01-05-2016 08:23 PM
Probabilistic validation of protein NMR chemical shift assignments
Probabilistic validation of protein NMR chemical shift assignments
Abstract
Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data . ARECA has been evaluated through its application to 26...
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01-03-2016 01:25 AM
[NMR paper] Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
J Biomol NMR. 2013 Apr 28;
Authors: Fritzsching KJ, Yang Y, Schmidt-Rohr K, Hong M
Abstract
We introduce a Python-based program that utilizes the large database of (13)C and (15)N chemical shifts in the Biological Magnetic...
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04-30-2013 10:21 PM
PACSY, a relational database management system for protein structure and chemical shift analysis
PACSY, a relational database management system for protein structure and chemical shift analysis
Abstract PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational...
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08-21-2012 02:04 AM
RefDB: Re-referenced Protein Chemical Shift Database
RefDB website
In case of the BMRB, it is known that a significant portion of depositions use different or non-IUPAC chemical shift reference standards. This lack of uniformity makes it difficult to extract sequence/structure relationships from chemical shifts. Nearly 40% of protein entries deposited in the BioMagResBank appear to have at least one assignment error. In addition, it evident that protein NMR spectroscopists are increasingly adhering to recommended IUPAC (13)C and (15)N chemical shift referencing conventions, however, approximately 20% of newly deposited protein entries in the...
gwnmr
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01-10-2012 06:28 PM
[NMR paper] 1H, 15N, and 13C backbone chemical shift assignments, secondary structure, and magnes
1H, 15N, and 13C backbone chemical shift assignments, secondary structure, and magnesium-binding characteristics of the Bacillus subtilis response regulator, Spo0F, determined by heteronuclear high-resolution NMR.
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 1H, 15N, and 13C backbone chemical shift assignments, secondary structure, and...
NMR chemical shift assignments of RNA oligonucleotides to expand the RNA chemical shift database
Linear Mode
