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 require many non-linear fitting parameters, thereby confounding assessment of accuracy. Moreover, novice CPMG experimentalists face an additional barrier because current software options lack an intuitive user interface and extensive documentation. Hence, we present the open-source software package GUARDD (Graphical User-friendly Analysis of Relaxation Dispersion Data), which is designed to organize, automate, and enhance the analytical procedures which operate on CPMG RD data (http://code.google.com/p/guardd/). This MATLAB-based program includes a graphical user interface, permits global fitting to multi-field, multi-temperature, multi-coherence data, and implements Ï? 2-mapping procedures, via grid-search and Monte Carlo methods, to enhance and assess fitting accuracy. The presentation features allow users to seamlessly traverse the large amount of results, and the RD Simulator feature can help design future experiments as well as serve as a teaching tool for those unfamiliar with RD phenomena. Based on these innovative features, we expect that GUARDD will fill a well-defined gap in service of the RD NMR community.
Content Type Journal Article
Category Article
Pages 1-12
DOI 10.1007/s10858-011-9589-y
Authors
Ian R. Kleckner, Biophysics Program, The Ohio State University, 484 West 12th Ave Room 776, Columbus, OH 43210, USA
Mark P. Foster, Biochemistry Department, The Ohio State University, 484 West 12th Ave Room 776, Columbus, OH 43210, USA
[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.
nmrlearner
News from NMR blogs
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12-21-2011 04:12 AM
A software framework for analysing solid-state MAS NMR data.
A software framework for analysing solid-state MAS NMR data.
A software framework for analysing solid-state MAS NMR data.
J Biomol NMR. 2011 Sep 28;
Authors: Stevens TJ, Fogh RH, Boucher W, Higman VA, Eisenmenger F, Bardiaux B, van Rossum BJ, Oschkinat H, Laue ED
Abstract
Solid-state magic-angle-spinning (MAS) NMR of proteins has undergone many rapid methodological developments in recent years, enabling detailed studies of protein structure, function and dynamics. Software development, however, has not kept pace with these advances...
nmrlearner
Journal club
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relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins
relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins
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...
nmrlearner
Journal club
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06-06-2011 12:53 AM
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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It's been over 6 weeks since my last post on this blog but don’t worry, I haven’t been idle. On the contrary, I have a very good excuse for this lack of posts: We all at Mestrelab have been working very hard trying to get version 6.0 of Mnova finished. Now I’m delighted to announce that we have done it and version 6.0 is finally available for download from our Web site. This is certainly a major upgrade of the software in which we have put a lot of work and passion. It brings a number of...
nmrlearner
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How to import NMR data to Origin software
Hi!
I have a little problem, I can't import NMR data (Bruker Avans 600MHz) to Origin 8.0 or 6.0 version. I am affraid that Bruker changed file format, I was able to do this with files from old Bruker 300MHz. Anybody know how to resolve it? Thanks for help!!
Fr
GUARDD: user-friendly MATLAB software for rigorous analysis of CPMG RD NMR data
Linear Mode
