sedphat

[ sedphat ] [ download ] [ sedphat help ] [ concepts for getting started ] [Experimental Protocols] [ tutorials ] [ troubleshooting and questions ] [ references ] [ sedfit

 

SEDPHAT  

is an extended version of Sedfit for the global analysis of sedimentation velocity, sedimentation equilibrium, and/or dynamic light scattering experiments.  At the same time, it is a stand-alone sedimentation equilibrium analysis software.  Further, isotherms of weight-average sedimentation coefficients or weight-average molar mass values can be incorporated into the analysis, as well as isothermal titration calorimetry isotherms and surface binding isotherms. All data types can be mixed and simultaneously fitted, and Sedphat can be used as a general platform the global analysis of interacting systems in different experiments.

Sedphat was written at the National Institutes of Health and is freely distributed without charge for research use. The program can be downloaded from here but it is also available directly from sedfitsedphat.nibib.nih.gov. However, this website was written by the author in his private capacity, and no official support or endorsement of NIH is intended and should be inferred.  disclaimer

The main purpose of this website is to provide information for using the software, such as an online help reference information, background information, and examples of what it does and how it can be used.   

 

upcoming workshops:

 

 

May 8 - 12, 2017 "Biophysical Methods for Protein Interactions" at the National Institutes of Health, Bethesda

by the Foundation of Advanced Education in the Sciences, NIH (http://events.r20.constantcontact.com/register/event?oeidk=a07edizq2xsf2e07af2&llr=k4uamblab). 

For topics covered, see https://sedfitsedphat.nibib.nih.gov/workshop/default.aspx#biophysicalworkshop

 

 

Please sign up to the SEDPHAT-L listserv for discussion of applications of SEDPHAT and questions of global analysis of ITC, AUC, and other biophysical techniques.  This forum reaches currently ~ 220 colleagues in the field of studying macromolecular interactions with biophysical methodology.

horizontal rule

 

The main features of Sedphat include: 

bulletsedimentation equilibrium: complete framework for global analysis of molar mass distributions, species analysis, self-associating proteins, and hetero-associations. Analysis features such as mass conservation constraints and multi-wavelength analysis are fully implemented. bulletsedimentation velocity:  global analysis of multiple sedimentation velocity data (multi-signal capable), with continuous size-distributions, discrete species and hybrid models, as well as protein self-association models.   bulletdynamic light scattering:  discrete and continuous distributions bulletsedimentation isotherms:  isotherms of weight-average s-values or Mw values can be analyzed with interacting systems models bulletisothermal titration calorimetry:  delta-H isotherms from titrations of heterogeneous interactions bulletsurface plasmon resonance: surface-binding equilibria as a function of analyte concentration (isotherms of steady-state signals), in direct binding or competition mode bullet

global analysis:  data sets from multiple experimental techniques can be combined in a global analysis.  Extensive data simulation and visualization tools aid in the experimental planning.  horizontal rule

 For AUC users, Sedphat will appear as a more powerful and flexible extension of Sedfit.  Therefore, for the analysis of AUC data, I suggest for new users to get a little bit familiar with the basics of Sedfit, even if the main goal is sedimentation equilibrium analysis.  The similarities with Sedfit include: 

bulletsame overall strategy of the sequence: loading data, selecting the model, fitting the model, saving the results bulletsame conventions to load the data and graphically determine fitting limits, meniscus and bottom, zoom and unzoom bullet

same display and copy options for saving results, data, and fits horizontal rule

Because Sedphat extends the data analysis to global analysis of multiple experiments, possibly of different kinds, much more powerful models are possible.  At the same time, however, the global analysis requires more complex structures for the data, the parameters, and their relationships.  The present Sedphat help web concentrates more on these issues, rather than, for example, the detailed user-interface issues that are described in great detail in the Sedfit help system.

Compared to Sedfit, the main differences of Sedphat are:

bullet

to facilitate global analysis of multiple experiments, the data can be save as 'experiments' (*.xp files) together with the local experimental and fitting parameters.  bullet

the parameters can be classified as global, shared local, or local parameters. bullet

all parameters in Sedphat are corrected to standard conditions (water, 20C).  This is in contrast to Sedfit, which is (almost) entirely in experimental parameters  bullet

concentration parameters and binding constants in Sedphat are in molar units, not signal units.  horizontal rule

You can find in this website

bullet

an introduction to the concepts of Sedphat for getting started bullet

an on-line reference for all menu functions bullet

instructions for downloading Sedphat

For further inquiries send an email to pschuck@helix.nih.gov (or see the contact information).  

 

horizontal rule

search SEDFIT and SEDPHAT websites

Google
SEDFIT/SEDPHAT
horizontal rule

DISCLAIMER STATEMENT:

The information contained herein is provided as a service with the understanding that the author makes no warranties, either expressed or implied, concerning the accuracy, completeness, reliability, or suitability of the information.