Literature DB >> 21618018

relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins.

Michael Bieri1, Edward J d'Auvergne, Paul R Gooley.   

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.

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Year:  2011        PMID: 21618018     DOI: 10.1007/s10858-011-9509-1

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  18 in total

1.  Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data.

Authors:  P Dosset; J C Hus; M Blackledge; D Marion
Journal:  J Biomol NMR       Date:  2000-01       Impact factor: 2.835

2.  FAST-Modelfree: a program for rapid automated analysis of solution NMR spin-relaxation data.

Authors:  Roger Cole; J Patrick Loria
Journal:  J Biomol NMR       Date:  2003-07       Impact factor: 2.835

3.  Direct measurement of the 15N CSA/dipolar relaxation interference from coupled HSQC spectra.

Authors:  Jennifer B Hall; Kwaku T Dayie; David Fushman
Journal:  J Biomol NMR       Date:  2003-06       Impact factor: 2.835

4.  The use of model selection in the model-free analysis of protein dynamics.

Authors:  Edward J d'Auvergne; Paul R Gooley
Journal:  J Biomol NMR       Date:  2003-01       Impact factor: 2.835

5.  Model-free model elimination: a new step in the model-free dynamic analysis of NMR relaxation data.

Authors:  Edward J d'Auvergne; Paul R Gooley
Journal:  J Biomol NMR       Date:  2006-06-22       Impact factor: 2.835

6.  Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm.

Authors:  Edward J d'Auvergne; Paul R Gooley
Journal:  Mol Biosyst       Date:  2007-05-17

7.  TEM-1 backbone dynamics-insights from combined molecular dynamics and nuclear magnetic resonance.

Authors:  Olivier Fisette; Sébastien Morin; Pierre-Yves Savard; Patrick Lagüe; Stéphane M Gagné
Journal:  Biophys J       Date:  2010-02-17       Impact factor: 4.033

8.  Backbone dynamics of the olfactory marker protein as studied by 15N NMR relaxation measurements.

Authors:  Rossitza K Gitti; Nathan T Wright; Joyce W Margolis; Kristen M Varney; David J Weber; Frank L Margolis
Journal:  Biochemistry       Date:  2005-07-19       Impact factor: 3.162

Review 9.  Using NMR to study fast dynamics in proteins: methods and applications.

Authors:  Paul J Sapienza; Andrew L Lee
Journal:  Curr Opin Pharmacol       Date:  2010-10-08       Impact factor: 5.547

10.  Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor.

Authors:  Edward J d'Auvergne; Paul R Gooley
Journal:  J Biomol NMR       Date:  2007-12-18       Impact factor: 2.835

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  28 in total

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2.  Effects of PRE and POST therapy drug-pressure selected mutations on HIV-1 protease conformational sampling.

Authors:  Jeffrey D Carter; Estrella G Gonzales; Xi Huang; Adam N Smith; Ian Mitchelle S de Vera; Peter W D'Amore; James R Rocca; Maureen M Goodenow; Ben M Dunn; Gail E Fanucci
Journal:  FEBS Lett       Date:  2014-06-28       Impact factor: 4.124

3.  The role of select subtype polymorphisms on HIV-1 protease conformational sampling and dynamics.

Authors:  Xi Huang; Manuel D Britto; Jamie L Kear-Scott; Christopher D Boone; James R Rocca; Carlos Simmerling; Robert Mckenna; Michael Bieri; Paul R Gooley; Ben M Dunn; Gail E Fanucci
Journal:  J Biol Chem       Date:  2014-04-17       Impact factor: 5.157

4.  NMR Analysis of Amide Hydrogen Exchange Rates in a Pentapeptide-Repeat Protein from A. thaliana.

Authors:  Shenyuan Xu; Shuisong Ni; Michael A Kennedy
Journal:  Biophys J       Date:  2017-05-23       Impact factor: 4.033

5.  Structural characterization of zinc-bound Zmp1, a zinc-dependent metalloprotease secreted by Clostridium difficile.

Authors:  Jeffrey T Rubino; Manuele Martinelli; Francesca Cantini; Andrea Castagnetti; Rosanna Leuzzi; Lucia Banci; Maria Scarselli
Journal:  J Biol Inorg Chem       Date:  2015-12-28       Impact factor: 3.358

6.  Dissecting Dynamic Allosteric Pathways Using Chemically Related Small-Molecule Activators.

Authors:  George P Lisi; Gregory A Manley; Heidi Hendrickson; Ivan Rivalta; Victor S Batista; J Patrick Loria
Journal:  Structure       Date:  2016-05-26       Impact factor: 5.006

7.  AMP-activated protein kinase β-subunit requires internal motion for optimal carbohydrate binding.

Authors:  Michael Bieri; Jesse I Mobbs; Ann Koay; Gavin Louey; Yee-Foong Mok; Danny M Hatters; Jong-Tae Park; Kwan-Hwa Park; Dietbert Neumann; David Stapleton; Paul R Gooley
Journal:  Biophys J       Date:  2012-01-18       Impact factor: 4.033

8.  Effects of Hinge-region Natural Polymorphisms on Human Immunodeficiency Virus-Type 1 Protease Structure, Dynamics, and Drug Pressure Evolution.

Authors:  Zhanglong Liu; Xi Huang; Lingna Hu; Linh Pham; Katye M Poole; Yan Tang; Brian P Mahon; Wenxing Tang; Kunhua Li; Nathan E Goldfarb; Ben M Dunn; Robert McKenna; Gail E Fanucci
Journal:  J Biol Chem       Date:  2016-08-30       Impact factor: 5.157

9.  Conformational dynamics of a G-protein α subunit is tightly regulated by nucleotide binding.

Authors:  David Goricanec; Ralf Stehle; Pascal Egloff; Simina Grigoriu; Andreas Plückthun; Gerhard Wagner; Franz Hagn
Journal:  Proc Natl Acad Sci U S A       Date:  2016-06-13       Impact factor: 11.205

10.  Allosteric Motions of the CRISPR-Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics.

Authors:  Kyle W East; Jocelyn C Newton; Uriel N Morzan; Yogesh B Narkhede; Atanu Acharya; Erin Skeens; Gerwald Jogl; Victor S Batista; Giulia Palermo; George P Lisi
Journal:  J Am Chem Soc       Date:  2020-01-09       Impact factor: 15.419

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