Re: [R] one-site competition data // curve fitting

From: Joerg van den Hoff <j.van_den_hoff_at_fzd.de>
Date: Tue, 08 Jul 2008 13:08:01 +0200

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



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