NMR spectroscopy is an indispensably powerful technique for the analysis of biomolecules under ambient conditions, both for structural- and functional studies. However, in practice the complexity of the technique has often frustrated its application by non-specialists. In this paper, we present CcpNmr version-3, the latest software release from the Collaborative Computational Project for NMR, for all aspects of NMR data analysis, including liquid- and solid-state NMR data. This software has been designed to be simple, functional and flexible, and aims to ensure that routine tasks can be performed in a straightforward manner. We have designed the software according to modern software engineering principles and leveraged the capabilities of modern graphics libraries to simplify a variety of data analysis tasks. We describe the process of backbone assignment as an example of the flexibility and simplicity of implementing workflows, as well as the toolkit used to create the necessary graphics for this workflow. The package can be downloaded from www.ccpn.ac.uk/v3-software/downloads and is freely available to all non-profit organisations.
Maximum occurrence analysis of protein conformations for different distributions of paramagnetic metal ions within flexible two-domain proteins
Maximum occurrence analysis of protein conformations for different distributions of paramagnetic metal ions within flexible two-domain proteins
Publication year: 2012
Source:Journal of Magnetic Resonance, Volume 215</br>
Claudio Luchinat, Malini Nagulapalli, Giacomo Parigi, Luca Sgheri</br>
Multidomain proteins are composed of rigid domains connected by (flexible) linkers. Therefore, the domains may experience a large degree of reciprocal reorientation. Pseudocontact shifts and residual dipolar couplings arising from one or more paramagnetic metals successively placed...
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03-09-2012 09:16 AM
Maximum occurrence analysis of protein conformations for different distributions of paramagnetic metal ions within flexible two-domain proteins
Maximum occurrence analysis of protein conformations for different distributions of paramagnetic metal ions within flexible two-domain proteins
Publication year: 2011
Source: Journal of Magnetic Resonance, Available online 30 December 2011</br>
Claudio*Luchinat, Malini*Nagulapalli, Giacomo*Parigi, Luca*Sgheri</br>
Multidomain proteins are composed of rigid domains connected by (flexible) linkers. Therefore, the domains may experience a large degree of reciprocal reorientation. Pseudocontact shifts and residual dipolar couplings arising from one or more paramagnetic metals successively...
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12-31-2011 10:40 AM
[KPWU blog] run CcpNmr Analysis on Mac
run CcpNmr Analysis on Mac
For Mac users, Fink provides an easy way to install “CcpNmr Analysis” and the dependent packages. Once you installed Fink, simply type ‘fink install ccpnmr-py26″ to get all required packaged installed for Mac OS. If you prefer using Python 2.7, then type “fink install ccpnmr-py27″ to install it. I am currently running the python 2.6 http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=278&subd=kpwu&ref=&feed=1
Go to KPWU blog to read complete post.
nmrlearner
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02-08-2011 08:02 AM
[KPWU blog] run CcpNmr Analysis on Mac
run CcpNmr Analysis on Mac
For Mac users, Fink provides an easy way to install “CcpNmr Analysis” and the dependent packages. Once you installed Fink, simply type ‘fink install ccpnmr-py26″ to get all required packaged installed for Mac OS. If you prefer using Python 2.7, then type “fink install ccpnmr-py27″ to install it. I am currently running the python 2.6 http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=278&subd=kpwu&ref=&feed=1
Go to KPWU blog to read complete post.
nmrlearner
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02-08-2011 07:54 AM
Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy
Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy
Abstract Long-range structural information derived from paramagnetic relaxation enhancement observed in the presence of a paramagnetic nitroxide radical is highly useful for structural characterization of globular, modular and intrinsically disordered proteins, as well as proteinā??protein and protein-DNA complexes. Here we characterized the conformation of a spin-label attached to the homodimeric protein CylR2 using a combination of X-ray crystallography, electron...
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01-31-2011 06:03 AM
Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy.
Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy.
Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy.
J Biomol NMR. 2011 Jan 28;
Authors: Gruene T, Cho MK, Karyagina I, Kim HY, Grosse C, Giller K, Zweckstetter M, Becker S
Long-range structural information derived from paramagnetic relaxation enhancement observed in the presence of a paramagnetic nitroxide radical is highly useful for structural characterization of...
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01-29-2011 12:35 PM
[NMR paper] An integrated platform for automated analysis of protein NMR structures.
An integrated platform for automated analysis of protein NMR structures.
Related Articles An integrated platform for automated analysis of protein NMR structures.
Methods Enzymol. 2005;394:111-41
Authors: Huang YJ, Moseley HN, Baran MC, Arrowsmith C, Powers R, Tejero R, Szyperski T, Montelione GT
Recent developments provide automated analysis of NMR assignments and three-dimensional (3D) structures of proteins. These approaches are generally applicable to proteins ranging from about 50 to 150 amino acids. In this chapter, we summarize progress...
CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis
Linear Mode
