A suite of programs called CAMRA (Computer Aided Magnetic Resonance Assignment) has been developed for computer assisted residue-specific assignments of proteins. CAMRA consists of three units: ORB, CAPTURE and PROCESS. ORB predicts NMR chemical shifts for unassigned proteins using a chemical shift database of previously assigned homologous proteins supplemented by a statistically derived chemical shift database in which the shifts are categorized according to their residue, atom and secondary structure type. CAPTURE generates a list of valid peaks from NMR spectra by filtering out noise peaks and other artifacts and then separating the derived peak list into distinct spin systems. PROCESS combines the chemical shift predictions from ORB with the spin systems identified by CAPTURE to obtain residue specific assignments. PROCESS ranks the top choices for an assignment along with scores and confidence values. In contrast to other auto-assignment programs, CAMRA does not use any connectivity information but instead is based solely on matching predicted shifts with observed spin systems. As such, CAMRA represents a new and unique approach for the assignment of protein NMR spectra. CAMRA will be particularly useful in conjunction with other assignment methods and under special circumstances, such as the assignment of flexible regions in proteins where sufficient NOE information is generally not available. CAMRA was tested on two medium-sized proteins belonging to the chemokine family. It was found to be effective in predicting the assignment providing a database of previously assigned proteins with at least 30% sequence identity is available. CAMRA is versatile and can be used to include and evaluate heteronuclear and three-dimensional experiments.
Backbone and Ile-?1, Leu, Val Methyl (1)H, (13)C and (15)N NMR chemical shift assignments for human interferon-stimulated gene 15 protein.
Backbone and Ile-?1, Leu, Val Methyl (1)H, (13)C and (15)N NMR chemical shift assignments for human interferon-stimulated gene 15 protein.
Backbone and Ile-?1, Leu, Val Methyl (1)H, (13)C and (15)N NMR chemical shift assignments for human interferon-stimulated gene 15 protein.
Biomol NMR Assign. 2011 May 5;
Authors: Yin C, Aramini JM, Ma LC, Cort JR, Swapna GV, Krug RM, Montelione GT
Human interferon-stimulated gene 15 protein (ISG15), also called ubiquitin cross-reactive protein (UCRP), is the first identified ubiquitin-like protein containing...
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[NMR paper] Magic-angle spinning solid-state NMR spectroscopy of the beta1 immunoglobulin binding domain of protein G (GB1): 15N and 13C chemical shift assignments and conformational analysis.
Magic-angle spinning solid-state NMR spectroscopy of the beta1 immunoglobulin binding domain of protein G (GB1): 15N and 13C chemical shift assignments and conformational analysis.
Related Articles Magic-angle spinning solid-state NMR spectroscopy of the beta1 immunoglobulin binding domain of protein G (GB1): 15N and 13C chemical shift assignments and conformational analysis.
J Am Chem Soc. 2005 Sep 7;127(35):12291-305
Authors: Franks WT, Zhou DH, Wylie BJ, Money BG, Graesser DT, Frericks HL, Sahota G, Rienstra CM
Magic-angle spinning...
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[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...
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11-24-2010 09:01 PM
NMR chemical shift assignments of a complex between SUMO-1 and SIM peptide derived fr
NMR chemical shift assignments of a complex between SUMO-1 and SIM peptide derived from the C-terminus of Daxx.
Related Articles NMR chemical shift assignments of a complex between SUMO-1 and SIM peptide derived from the C-terminus of Daxx.
Biomol NMR Assign. 2010 Oct 7;
Authors: Naik MT, Chang CC, Naik NM, Kung CC, Shih HM, Huang TH
Small Ubiquitin-like MOdifiers (SUMOs) are ubiquitin-like proteins known to covalently modify large number of cellular proteins. The mammalian SUMO family includes four paralogues, SUMO-1 through SUMO-4....
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[NMR paper] 1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary struct
1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary structure of glutamine-binding protein of Escherichia coli.
Related Articles 1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary structure of glutamine-binding protein of Escherichia coli.
J Biomol NMR. 1997 Feb;9(2):167-80
Authors: Yu J, Simplaceanu V, Tjandra NL, Cottam PF, Lukin JA, Ho C
1H, 13C, and 15N NMR assignments of the backbone atoms and beta-carbons have been made for liganded glutamine-binding protein (GlnBP) of Escherichia...
[NMR paper] Computer-aided assignment of the 1H-NMR spectrum of the viral-protein-genome-linked p
Computer-aided assignment of the 1H-NMR spectrum of the viral-protein-genome-linked polypeptide from cowpea mosaic virus.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles Computer-aided assignment of the 1H-NMR spectrum of the viral-protein-genome-linked polypeptide from cowpea mosaic virus.
Eur J Biochem. 1990 Jul 5;190(3):583-91
Authors: van de Ven FJ, Lycksell PO, van Kammen A, Hilbers CW
The 1H-NMR spectrum of the...
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A probabilistic approach for validating protein NMR chemical shift assignments
Abstract It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program...
CAMRA: chemical shift based computer aided protein NMR assignments.
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