NESSY

From relax wiki
Jump to: navigation, search
The NESSY logo.

The NESSY relaxation dispersion software is supported in relax. NESSY input project files can be created through a single relax user function, after all base data has been loaded. Note that NESSY is in maintenance mode - the project is currently dormant with no active developers.

Details

Website

The original NESSY website is https://nmr-nessy.sourceforge.io/, and the SourceForge page is https://sourceforge.net/projects/nmr-nessy/.

Overview

From the NESSY website (with light editing):

NESSY is an open source software to analyse NMR relaxation dispersion data of either CPMG or R 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 (R2,eff) and performs model selection between different relaxation dispersion models.

Features:

  • Calculation of effective transverse relaxation rate (R2,eff)
  • Models for 1 - 9 exchanging states
  • Analysis of multiple data set (global fit)
  • Analysis of CPMG relaxation dispersion experiments
  • Analysis of R 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 (Δω)
  • 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:
  • 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 12.3.1 from March 2012.

Reference

  • Bieri, M. and Gooley, P. (2011). Automated NMR relaxation dispersion data analysis using NESSY. BMC Bioinformatics, 12, 1-10. (DOI: 10.1186/1471-2105-12-421)

Usage in relax

The following user function are provided for NESSY support within relax:

See also