Comparison of dispersion analysis software

Diverse software exists for analysing relaxation dispersion data. The following is a list of the officially released software which you can use instead of relax:

CPMGFit
Art Palmer's original dispersion analysis software at http://www.palmer.hs.columbia.edu/software/cpmgfit.html.
cpmg_fit
Dmitry Korzhnev's dispersion software available upon request.
CATIA
Flemming Hansen's dispersion software at http://www.biochem.ucl.ac.uk/hansen/catia/. The reference is Hansen et al. (2008).
NESSY
Michael Bieri's dispersion software at http://home.gna.org/nessy/. The reference is Bieri and Gooley (2011).
GUARDD
Ian Kleckner's dispersion software at http://code.google.com/p/guardd/. The reference is Kleckner and Foster (2012).
ShereKhan
See the web server at http://sherekhan.bionmr.org/. The reference is Mazur et al. (2013).
GLOVE
Peter Wright's dispersion software at http://www.scripps.edu/wright/. The reference is Sugase et al. (2013).
chemex
Guillaume Bouvignies' dispersion software which can be found at http://code.google.com/p/chemex/.

There is currently support in relax for generating the input files for CPMGFit, CATIA, NESSY, and ShereKhan and for running CPMGFit and CATIA from within relax.

The features of the different software are compared in Table 11.4 on page [*]. Note that this table is likely to be incomplete so please see the websites of the respective software for an up to date list of features. The aim of this table is to provide a fair comparison between all of the available dispersion software. Therefore if you do find deficiencies or errors in this table please report these either to the relax users mailing list at ``relax-users at gna.org'', submit a bug report (see section 3.3 on page [*]), or send a private message to one of the relax developers (http://gna.org/project/memberlist.php?group=relax) so that the details can be corrected.

Table 11.4: Comparison of the features for the different dispersion software.

 




 
  CPMGFit cpmg_fit CATIA NESSY GUARDD ShereKhan GLOVE chemex relax
 


 
Dispersion models  

 
Base models  
R2eff/R1ρ'   - - - -
No Rex   - - - -

 
Single quantum (SQ) CPMG-type  
LM63   - - - -
LM63 3-site   - - - - - -
CR72   - - - -
IT99   - - - - - -
TSMFK01   - - - - - - - -
B14   - - - - - - - -
NS 2-site   - - - ? -

 
MMQ (SQ, ZQ, DQ, & MQ) CPMG-type  
MMQ CR72   - - - - ? -
NS MMQ 2-site   - - - - - ? -
NS MMQ 3-site linear   - - - - - ? -
NS MMQ 3-site   - - - - - ? -

 
R1ρ-type  
M61   - - - - - - - -
DPL94   - - - - - - - -
TP02   - - - - - - -
TAP03   - - - - - - - -
TP04   - - - - - - - - -
MP05   - - - - - - - -
BK13   - - - - - - - - -
NS R1ρ 2-site   - - - - - ? -
NS R1ρ 3-site linear   - - - - - - -
NS R1ρ 3-site   - - - - - - -

 
General features  
Parallelisation via MPI for running on clusters   - - - - - - - -
Off-resonance effects (CPMG-type data)   - - - - - - - -
Off-resonance effects ( R1ρ-type data)   - - - - - - -
Support for TROSY-type data   - - - - - - - -
Support for CEST-type data   - - - - - - - -
Support for scalar coupling effects   - - - - - - - -
Arrhenius / Van't Hoff analysis   - - - - - -
Dispersion data back calculation (BC)   - - - - -


 
User interface  
Graphical user interface (GUI)   - - - - - -
Web user interface (Web UI)   - - - - - - - -
Scripting user interface (Script UI)   - - - -
Shell interface   - - - - - - -
Temperature and field-dependent simulator  
UI for experimental planning (data BC)   - - - - - - - -

 
Optimisation  
Grid search algorithm   - - -
Grid search (via scripting)   - - - - - - - -
Nelder-Mead simplex algorithm   - - - - - - - -
Levenberg-Maquardt algorithm   - -
Numeric gradient approximation   - -
Logarithmic-barrier constraint algorithm   - - - - - - -
MATLAB interior-point black magic   - - - - - - - -
Visualisation of the chi-squared space   - - - - - - -

 
Error propagation  
Covariance matrix (lowest quality)   - - -
Jackknife simulations (for missing errors)   - - - - - - -
Bootstrapping simulations (false errors)   - - - - - - - - -
Monte Carlo simulations (gold standard)   - - -

 
Inbuilt statistical comparisons  
Akaike's Information Criterion (AIC)   - - - - - - -
Small sample size AIC (AICc)   - - - - - - -
Bayesian Information Criterion (BIC)   - - - - - - - -
F-testing (ANOVA statistics)   - - - - - - -

 
Data and model testing  
Insignificant dispersion curve tests   - - - - - - -
Model elimination tests   - - - - - - - -

 
Programming languages  
Python   - - - - -
C   - - - - -
Perl   - - - - - - - -
MATLAB   - - - - - - - -
FORTRAN   - - - - - - - -
Ruby on Rails   - - - - - - - -

 
Open source licencing  
GNU General Public Licence (version 2+)   - - - - - - - -
GNU General Public Licence (version 3+)   - - - - -
Open source infrastructure   - - - - -
Proprietary   - - - - -
 
 

The relax user manual (PDF), created 2016-10-28.