Related ArticlesNvAssign: protein NMR spectral assignment with NMRView.
Bioinformatics. 2004 May 1;20(7):1201-3
Authors: Kirby NI, DeRose EF, London RE, Mueller GA
MOTIVATION: Nuclear magnetic resonance (NMR) protein studies rely on the accurate assignment of resonances. The general procedure is to (1) pick peaks, (2) cluster data from various experiments or spectra, (3) assign peaks to the sequence and (4) verify the assignments with the spectra. Many algorithms already exist for automating the assignment process (step 3). What is lacking is a flexible interface to help a spectroscopist easily move from clustering (step 2) to assignment algorithms (step 3) and back to verification of the algorithm output with spectral analysis (step 4). RESULTS: A software module, NvAssign, was written for use with NMRView. It is a significant extension of the previous CBCA module. The module provides a flexible interface to cluster data and interact with the existing assignment algorithms. Further, the software module is able to read the results of other algorithms so that the data can be easily verified by spectral analysis. The generalized interface is demonstrated by connecting the clustered data with the assignment algorithms PACES and MONTE using previously assigned data for the lyase domain of DNA polymerase lambda. The spectral analysis program NMRView is now able to read the output of these programs for simplified analysis and verification. AVAILABILITY: NvAssign is available from http://dir.niehs.nih.gov/dirnmr/nvassign
Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data
Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data
Abstract One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY...
nmrlearner
Journal club
0
06-27-2011 04:30 AM
[Question from NMRWiki Q&A forum] How to pick peaks manually in nmrview?
How to pick peaks manually in nmrview?
Is there any way to pick peaks manually in nmrview using the red/black cursors?
Check if somebody has answered this question on NMRWiki QA forum
nmrlearner
News from other NMR forums
0
01-26-2011 04:21 AM
[Question from NMRWiki Q&A forum] Can you pick peaks manually in nmrview?
Can you pick peaks manually in nmrview?
Is there any way to pick peaks manually in nmrview using the red/black cursors?
Check if somebody has answered this question on NMRWiki QA forum
nmrlearner
News from other NMR forums
0
01-25-2011 04:10 AM
[NMR paper] Resonance assignment of proteins with high shift degeneracy based on 5D spectral info
Resonance assignment of proteins with high shift degeneracy based on 5D spectral information encoded in G2FT NMR experiments.
Related Articles Resonance assignment of proteins with high shift degeneracy based on 5D spectral information encoded in G2FT NMR experiments.
J Am Chem Soc. 2005 Apr 6;127(13):4554-5
Authors: Atreya HS, Eletsky A, Szyperski T
A suite of novel (5,3)D G2FT triple resonance NMR experiments encoding highly resolved 5D spectral information is presented for sequential resonance assignment of proteins exhibiting high chemical...
nmrlearner
Journal club
0
11-25-2010 08:21 PM
[NMR paper] RESCUE: an artificial neural network tool for the NMR spectral assignment of proteins
RESCUE: an artificial neural network tool for the NMR spectral assignment of proteins.
Related Articles RESCUE: an artificial neural network tool for the NMR spectral assignment of proteins.
J Biomol NMR. 1999 Sep;15(1):15-26
Authors: Pons JL, Delsuc MA
The assignment of the 1H spectrum of a protein or a polypeptide is the prerequisite for advanced NMR studies. We present here an assignment tool based on the artificial neural network technology, which determines the type of the amino acid from the chemical shift values observed in the 1H...
nmrlearner
Journal club
0
11-18-2010 08:31 PM
[NMR paper] 1H NMR studies of human lysozyme: spectral assignment and comparison with hen lysozym
1H NMR studies of human lysozyme: spectral assignment and comparison with hen lysozyme.
Related Articles 1H NMR studies of human lysozyme: spectral assignment and comparison with hen lysozyme.
Biochemistry. 1990 Aug 7;29(31):7201-14
Authors: Redfield C, Dobson CM
Complete main-chain (NH and alpha CH) 1H NMR assignments are reported for the 130 residues of human lysozyme, along with extensive assignments for side-chain protons. Analysis of 2-D NOESY experiments shows that the regions of secondary structure for human lysozyme in solution are...
nmrlearner
Journal club
0
08-21-2010 11:04 PM
NMRView Installation Woes
I am trying to install NMRViewJava on my Fedora Core 5 laptop and was wondering if anyone has had problems with the izpack software. The installer opens and then stalls halfway though the process both in su and normal modes. Thanks for the help in advance.
R2-D2
NMR software
2
07-05-2006 04:20 AM
NvAssign: protein NMR spectral assignment with NMRView
NvAssign: protein NMR spectral assignment with NMRView.
http://dir.niehs.nih.gov/dirnmr/nvassign/manual/images/examinePeaks.jpg
Designed by Kirby NI, DeRose EF, London RE, Mueller GA.
Laboratory of Structural Biology, MR-01, National Institute of Environmental Health Sciences, National Institutes of Health, Box 12233, Research Triangle Park, NC 27709, USA.
Published in Bioinformatics. 2004 May 1;20(7):1201-3. Epub 2004 Feb 10.
NvAssign: protein NMR spectral assignment with NMRView.
Linear Mode
