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.

A general introduction to the study of protein interactions by analytical ultracentrifugation can be found at the website of our lab at NIH (DMAS/LCIMB/NIBIB). This includes an introduction to the general principles of AUC and detailed experimental protocols.

for upcoming workshops: see https://sedfitsedphat.nibib.nih.gov/workshop/default.aspx

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 several hundred colleagues in the field of studying macromolecular interactions with biophysical methodology.

The main features of Sedphat include:

sedimentation 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.

sedimentation 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.

dynamic light scattering: discrete and continuous distributions

sedimentation isotherms: isotherms of weight-average s-values or Mw values can be analyzed with interacting systems models

isothermal titration calorimetry: delta-H isotherms from titrations of heterogeneous interactions

surface plasmon resonance: surface-binding equilibria as a function of analyte concentration (isotherms of steady-state signals), in direct binding or competition mode

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.

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:

same overall strategy of the sequence: loading data, selecting the model, fitting the model, saving the results

same conventions to load the data and graphically determine fitting limits, meniscus and bottom, zoom and unzoom

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

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:

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

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

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

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

You can find in this website

an introduction to the concepts of Sedphat for getting started

an on-line reference for all menu functions

instructions for downloading Sedphat

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

search SEDFIT and SEDPHAT websites