Hello everyone, I have biological data from a competition experiment where a free ligand is titrated against the binding of a protein. Now, I would like to fit a standard on-site binding curve to this data in order to obtain the IC50 and Kd values. Unfortunately I have not been able to find a package/function which allows such a fitting and calculates the results. Does anyone know if there is a suitable package available and which function to apply? Thanks a lot. Cheers Thiemo Schreiber [[alternative HTML version deleted]]
On Mon, Jul 07, 2008 at 11:15:57AM +0200, Thiemo Schreiber wrote:> Hello everyone, > > I have biological data from a competition experiment where a free ligand is titrated against the binding of a protein. > > Now, I would like to fit a standard on-site binding curve to this data in order to obtain the IC50 and Kd values. > Unfortunately I have not been able to find a package/function which allows such a fitting and calculates the results. > > > Does anyone know if there is a suitable package available and which function to apply? > > Thanks a lot. > > Cheers > Thiemo Schreiber > [[alternative HTML version deleted]]this is probably what you are looking for: let x = vector of free ligand concenctrations y = vector of correspondng spec. protein bindings be defined in the R workspace. than use res <- nls( y ~ (x * Bmax) / (x + Kd), start = list(Bmax=, Kd=)) (providing some sensible start values for the free parameters , of course) cf. `nls' manpage for details
Check out the drc package. On Mon, Jul 7, 2008 at 5:15 AM, Thiemo Schreiber <schreibe at biochem.mpg.de> wrote:> Hello everyone, > > I have biological data from a competition experiment where a free ligand is titrated against the binding of a protein. > > Now, I would like to fit a standard on-site binding curve to this data in order to obtain the IC50 and Kd values. > Unfortunately I have not been able to find a package/function which allows such a fitting and calculates the results. > > > Does anyone know if there is a suitable package available and which function to apply? > > Thanks a lot. > > Cheers > Thiemo Schreiber > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >