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This website provides information on Sedfit, a software for the analysis of analytical ultracentrifugation and other hydrodynamic data, written at the National Institutes of Health and distributed without charge for research use. The program can be downloaded from here, and it is also available directly from sedfitsedphat.nibib.nih.gov, or it can be sent as an email attachment from the author on request). 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.
The main purpose of this website is to provide information for using the software, such as an online help reference information, and background information (tutorials) on direct boundary modeling, FAQs, references, examples and more. See the disclaimer.
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.
May 16 - 20, 2016 "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=a07eb5otzc291e524eb&llr=k4uamblab).
For topics covered, see https://sedfitsedphat.nibib.nih.gov/workshop/default.aspx#biophysicalworkshop
September 19 - 23, 2016 "Workshop for the hydrodynamic and thermodynamic analysis of biological macromolecules and their interactions with SEDFIT and SEDPHAT" at the International Institute of Molecular and Cell Biology in Warsaw, Poland
Organized by Roman Szczepanowski. For general info, topics covered and registration see http://www.iimcb.gov.pl/events.html#ev2016
Please join the Sedfit Users Group email list (reaches currently > 600 AUC users) for technical advice and discussions with other users on software issues and applications. You can also sign up to the SEDPHAT-L listserv for discussion of applications of SEDPHAT and questions of global analysis of ITC, AUC, DLS, SPR, and other biophysical techniques.
The main features of Sedfit include:
numerous statistical functions, loading options, and general purpose tools
extension to global analysis in Sedphat
is closely related to Sedphat,
which provides global modeling capability for both sedimentation equilibrium
and sedimentation velocity data. It also can serve as a platform for
the global analysis of a variety of isotherms from different biophysical
A snapshot from the direct boundary modeling of data from a sample of IgG, analyzed with a c(s) distribution of Lamm equation solutions illustrates the rich information contained in sedimentation velocity data.
This example also illustrates some of the main ideas of Sedfit: loading data from the entire sedimentation process, use of systematic noise decomposition (and subtraction), modeling with finite element solutions of the Lamm equation. If we expand the scale of the continuous sedimentation distribution c(s) with maximum entropy regularization shown above, it can be seen that the c(s) analysis reveals the presence of several oligomeric species and a smaller species:
Similarly, the analysis of data from a BSA sample
shows the presence of dimer and trimer in the sedimentation coefficient distribution c(s)
Transformation to a molar mass distribution (assuming that all species have a similar frictional ratio) is consistent with the oligomeric BSA species:
Analyses free of scale-relation ship assumptions of similar frictional ratios are available, such as the two-dimensional size-and-shape distribution c(s,f), c(s,M), and the general c(s,*).
Sedfit offers several different options for utilizing different prior knowledge on the sample under study (such as the number of discrete species, a self-association model, etc.). More information on these examples can be found in the step-by-step tutorial (BSA) and the example for using Sedfit (IgG).
For questions please contact the Sedfit Users Group email list .
search SEDFIT and SEDPHAT websites
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.
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