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
NMR software
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01-10-2012 06:28 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.
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...
[NMR paper] Influence of the completeness of chemical shift assignments on NMR structures obtaine
Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment.
Related Articles Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment.
J Struct Funct Genomics. 2003;4(2-3):179-89
Authors: Jee J, Güntert P
Reliable automated NOE assignment and structure calculation on the basis of a largely complete, assigned input chemical shift list and a list of unassigned NOESY cross peaks has recently become feasible for routine NMR protein...
nmrlearner
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11-24-2010 09:01 PM
[NMR paper] Improving the accuracy of NMR structures of DNA by means of a database potential of m
Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base-base positional interactions.
Related Articles Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base-base positional interactions.
J Am Chem Soc. 2001 May 2;123(17):3903-18
Authors: Kuszewski J, Schwieters C, Clore GM
NMR structure determination of nucleic acids presents an intrinsically difficult problem since the density of short interproton distance contacts is relatively low...
nmrlearner
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11-19-2010 08:32 PM
[Question from NMRWiki Q&A forum] How to plot chemical shift predictions obtained form SPARTA?
How to plot chemical shift predictions obtained form SPARTA?
Dear friends,
I had a mutation in my protein and now I have some amino acids around mutation remained unassigned. To get a way to find the missing peaks I modelled the mutated protein with modeller and out of the pdb file I got the chemical shift predictions using SPARTA. Now that I have chemical shift predictions I want to plot them like a spectra and overlay them to my real spectra to see if it will help me to assign some of the missing peaks. I know for solid-state NMR there is a software, but what about solution NMR?
...
nmrlearner
News from other NMR forums
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11-18-2010 06:16 PM
[NMR paper] Application of 1H NMR chemical shifts to measure the quality of protein structures.
Application of 1H NMR chemical shifts to measure the quality of protein structures.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Application 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...
nmrlearner
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08-22-2010 03:41 AM
[Stan NMR blog] Books about Patents and Intellectual Property
Books about Patents and Intellectual Property
BOOKS LIST: This large collection starts with 30 titles. Links to Amazon.
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ChemSpider - Database of Chemical Structures and Property Predictions
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