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Created an article for the NESSY software.
The NESSY relaxation dispersion software is supported in relax, in that relax can create NESSY input files. Note that NESSY is in maintenance mode - the project is currently dormant with no active developers.
== Details ==
=== Website ===
The original NESSY website is http://cumc.columbia.edu/dept/gsas/biochem//labs/palmer/software/modelfree.html.
=== Overview ===
From the NESSY website (with light editing):
{{quote|text=NESSY is an open source software to analyse NMR relaxation dispersion data of either CPMG or {{:R1rho}} dispersion experiments. The graphical interface enables simple management of large experimental data sets and simple and automated analysis. NESSY automatically calculates effective transverse relaxation rate ({{:R2eff}}) and performs model selection between different relaxation dispersion models.
Features:
* Calculation of effective transverse relaxation rate ({{:R2eff}})
* Models for 1 - 9 exchanging states
* Analysis of multiple data set (global fit)
* Analysis of CPMG relaxation dispersion experiments
* Analysis of {{:R1rho}} spin lock relaxation dispersion experiments
* Model-selection between different models
* Akaike information criteria (AIC) model selection
* F-test for model selection
* Grid search for estimation of parameters
* Chi2 curvefit and model selection
* Levenberg-Marquardt algorithm (least squares curve fitting)
* Monte Carlo simulations for estimation of uncertainities of extracted parameters
* Extraction of exchange rate ({{:Rex}}), exchange konstant ({{:kex}}), population of exchanging states ({{:pA}}, {{:pB}}), chemical shift differences ({{:deltaomega}})
* Color and width coded structures (PDB)
* Calculation of Free Energy
* van't Hoff analysis (linear and non-linear model)
* Transition state theory (using Eyring equation)
* Hydrogen-Deuterium (H/D) exchange
* 2D and 3D plotting
* Creation of energy landscapes
Compatibility:
* NESSY runs on Windows, Mac and Linux operating systems
* Written in Python for maximal performance
* Import of peak lists:
** Space or tabulator separated
** Semicolon separated
** [[CcpNmr]]
** [[Sparky]]
** [[XEASY]]
** [[NMRView]]
** any text file
* Import of VD lists (Bruker)
* Import of Bruker Protein Dynamics Center Project
* [[PyMOL]]
* Excel, OpenOffice...
Results generated by NESSY:
* Plots in PNG, SVG, PS, EPS and PDF format (see following points)
* Exchange constant {{:kex}}
* Exchange rate {{:Rex}}
* Population of exchanging states ({{:pA}}, {{:pB}})
* Shift differences
* Curvefit to different models
* Model selection
* CSV file of results for Excel, OpenOffice...
* Colour coded structures (using [[PyMOL]])
}}
=== Authors ===
* Michael Bieri.
=== Version ===
The last release was {{Current version NESSY}} from March 2012.
=== Reference ===
* {{#lst:Citations|BieriGooley11}}
== Usage in relax ==
The following user function are provided for NESSY support within relax:
* [http://www.nmr-relax.com/manual/relax_disp_nessy_input relax_disp.nessy_input]
== See also ==
[[Category:Relaxation dispersion analysis]]
[[Category:Software]]
== Details ==
=== Website ===
The original NESSY website is http://cumc.columbia.edu/dept/gsas/biochem//labs/palmer/software/modelfree.html.
=== Overview ===
From the NESSY website (with light editing):
{{quote|text=NESSY is an open source software to analyse NMR relaxation dispersion data of either CPMG or {{:R1rho}} dispersion experiments. The graphical interface enables simple management of large experimental data sets and simple and automated analysis. NESSY automatically calculates effective transverse relaxation rate ({{:R2eff}}) and performs model selection between different relaxation dispersion models.
Features:
* Calculation of effective transverse relaxation rate ({{:R2eff}})
* Models for 1 - 9 exchanging states
* Analysis of multiple data set (global fit)
* Analysis of CPMG relaxation dispersion experiments
* Analysis of {{:R1rho}} spin lock relaxation dispersion experiments
* Model-selection between different models
* Akaike information criteria (AIC) model selection
* F-test for model selection
* Grid search for estimation of parameters
* Chi2 curvefit and model selection
* Levenberg-Marquardt algorithm (least squares curve fitting)
* Monte Carlo simulations for estimation of uncertainities of extracted parameters
* Extraction of exchange rate ({{:Rex}}), exchange konstant ({{:kex}}), population of exchanging states ({{:pA}}, {{:pB}}), chemical shift differences ({{:deltaomega}})
* Color and width coded structures (PDB)
* Calculation of Free Energy
* van't Hoff analysis (linear and non-linear model)
* Transition state theory (using Eyring equation)
* Hydrogen-Deuterium (H/D) exchange
* 2D and 3D plotting
* Creation of energy landscapes
Compatibility:
* NESSY runs on Windows, Mac and Linux operating systems
* Written in Python for maximal performance
* Import of peak lists:
** Space or tabulator separated
** Semicolon separated
** [[CcpNmr]]
** [[Sparky]]
** [[XEASY]]
** [[NMRView]]
** any text file
* Import of VD lists (Bruker)
* Import of Bruker Protein Dynamics Center Project
* [[PyMOL]]
* Excel, OpenOffice...
Results generated by NESSY:
* Plots in PNG, SVG, PS, EPS and PDF format (see following points)
* Exchange constant {{:kex}}
* Exchange rate {{:Rex}}
* Population of exchanging states ({{:pA}}, {{:pB}})
* Shift differences
* Curvefit to different models
* Model selection
* CSV file of results for Excel, OpenOffice...
* Colour coded structures (using [[PyMOL]])
}}
=== Authors ===
* Michael Bieri.
=== Version ===
The last release was {{Current version NESSY}} from March 2012.
=== Reference ===
* {{#lst:Citations|BieriGooley11}}
== Usage in relax ==
The following user function are provided for NESSY support within relax:
* [http://www.nmr-relax.com/manual/relax_disp_nessy_input relax_disp.nessy_input]
== See also ==
[[Category:Relaxation dispersion analysis]]
[[Category:Software]]