Abstract Investigation of protein dynamics on the ps-ns and μs-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying protein dynamics at atomic resolution. Analysis of relaxation data using model-free analysis can be a tedious and time consuming process, which requires good knowledge of scripting procedures. The software relaxGUI was developed for fast and simple model-free analysis and is fully integrated into the software package relax. It is written in Python and uses wxPython to build the graphical user interface (GUI) for maximum performance and multi-platform use. This software allows the analysis of NMR relaxation data with ease and the generation of publication quality graphs as well as color coded images of molecular structures. The interface is designed for simple data analysis and management. The software was tested and validated against the command line version of relax.
Content Type Journal Article
Pages 1-9
DOI 10.1007/s10858-011-9509-1
Authors
Michael Bieri, Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
Edward J. dâ??Auvergne, Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
Paul R. Gooley, Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
[KPWU blog] GUARDD: user-friendly MATLAB software for rigorous analysis of CPMG RD NMR data
GUARDD: user-friendly MATLAB software for rigorous analysis of CPMG RD NMR data
There is an article published at Journal of Biomolecular NMR recently which describes a package of MATLAB scripts to analyze CPMG relaxation dispersion NMR data. I haven’t done CPMG RD experiments on my target proteins, however, I know the analysis of CPMG RD data is not trivial. This program, GUARDD, seems to be a very http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=629&subd=kpwu&ref=&feed=1
Go to KPWU blog to read complete post.
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12-21-2011 04:12 AM
GUARDD: user-friendly MATLAB software for rigorous analysis of CPMG RD NMR data
GUARDD: user-friendly MATLAB software for rigorous analysis of CPMG RD NMR data
Abstract Molecular dynamics are essential for life, and nuclear magnetic resonance (NMR) spectroscopy has been used extensively to characterize these phenomena since the 1950s. For the past 15 years, the Carr-Purcell Meiboom-Gill relaxation dispersion (CPMG RD) NMR experiment has afforded advanced NMR labs access to kinetic, thermodynamic, and structural details of protein and RNA dynamics in the crucial μs-ms time window. However, analysis of RD data is challenging because datasets are often large and...
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12-13-2011 02:46 AM
Paramagnetic relaxation enhancement to improve sensitivity of fast NMR methods: application to intrinsically disordered proteins
Paramagnetic relaxation enhancement to improve sensitivity of fast NMR methods: application to intrinsically disordered proteins
Abstract We report enhanced sensitivity NMR measurements of intrinsically disordered proteins in the presence of paramagnetic relaxation enhancement (PRE) agents such as Ni2+-chelated DO2A. In proton-detected 1H-15N SOFAST-HMQC and carbon-detected (H-flip)13CO-15N experiments, faster longitudinal relaxation enables the usage of even shorter interscan delays. This results in higher NMR signal intensities per units of experimental time, without adverse line...
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10-21-2011 10:04 PM
relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and ?s motion of proteins.
relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and ?s motion of proteins.
relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and ?s motion of proteins.
J Biomol NMR. 2011 May 27;
Authors: Bieri M, d'Auvergne EJ, Gooley PR
Investigation of protein dynamics on the ps-ns and ?s-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying...
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Journal club
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05-28-2011 06:50 PM
Simple tests for the validation of multiple field spin relaxation data
Simple tests for the validation of multiple field spin relaxation data
Abstract 15N spin relaxation data is widely used to extract detailed dynamic information regarding bond vectors such as the amide Nâ??H bond of the protein backbone. Analysis is typically carried using the Lipariâ??Szabo model-free approach. Even though the original model-free equation can be determined from single field R 1, R 2 and NOE, over-determination of more complex motional models is dependent on the recording of multiple field datasets. This is especially important for the characterization of conformational...
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01-09-2011 12:46 PM
[NMR paper] Analysis of slow interdomain motion of macromolecules using NMR relaxation data.
Analysis of slow interdomain motion of macromolecules using NMR relaxation data.
Related Articles Analysis of slow interdomain motion of macromolecules using NMR relaxation data.
J Am Chem Soc. 2001 May 2;123(17):3953-9
Authors: Baber JL, Szabo A, Tjandra N
The interpretation of NMR relaxation data for macromolecules possessing slow interdomain motions is considered. It is shown how the "extended model-free approach" can be used to analyze (15)N backbone relaxation data acquired at three different field strengths for Xenopus Ca(2+)-ligated...
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11-19-2010 08:32 PM
[Question from NMRWiki Q&A forum] What software can copy peak assignments for 2D T1 and T2 relaxation rate data analysi
What software can copy peak assignments for 2D T1 and T2 relaxation rate data analysis?
Hello,
I'm currently processing a large amount of T1 and T2 spectra in NMRDraw. I've been looking for a way to copy my peak assignments from one spectrum onto to the others so that I can quickly and accurately match height and volume values, but I've had little luck so far. Is it possible to manipulate the assignment tables to achieve this goal? NMRPipe and its associated applications are all very new to me at this point, so any information that may expand my general knowledge of the program or...
relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins
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