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Re: st: one/two-site competitive binding ado


From   David Airey <david.airey@Vanderbilt.Edu>
To   statalist@hsphsun2.harvard.edu
Subject   Re: st: one/two-site competitive binding ado
Date   Thu, 17 Apr 2003 10:21:41 -0500

Joseph Coveney kindly replied:

David Airey asked, "Has anyone ado files to perform nl regression models for one and
two site competitive binding assays? There are several other pharmacological assays in
GraphPad Prism 3.0 that I wondered if anyone has duplicated in Stata?"

In the first volume of Stata Technical Bulletin Reprints, pp. 68-73 and continuing pp. 73-
76, Paul Geiger provided descriptions of using Stata for radioimmunoassay ligand-
binding analysis. This would be one-site binding. The program he used was an early
version of a nonlinear least-squares regression ado-file in Stata, but an analogous setup
using the current -nl- ought to be straightforward.

If you have the nonlinear function written out for two-site binding, then it ought to be
fairly easy to implement in Stata using -nl- or even -ml-. The latter has advantages in a
-cluster()- option; see the FAQ by Weihua Guan at
www.stata.com/support/faqs/stat/nl_ml.html .

I'm not sure what GraphPad Prism 3.0 has for the other pharmacological assays. In
general, if the functions are available, then setting up the proper ado-file to be called by
-nl- will be feasible.
Thanks for this information. I'll likely give one of these equations a whirl to compare results. Others in the lab uses Motulsky's GraphPad prism because it's easy to use and the documentation is well done if full of typos. Be nice to have extended capabilities present in Stata that are not present in Prism.

From what I can tell, Prism 3.0 has several built in (and modifiable) classic equations, such as:

1. one site binding (hyperbola)

Y = Bmax * X
--------
Kd + X

two site binding

Y = Bmax1 * X Bmax2 * X
--------- + ---------
Kd1 + X Kd2 + X

2. sigmoidal dose-response

(top - bottom)
Y = bottom + --------------------
1 + 10^(logEC50 - X)

3. sigmoidal dose-response (variable slope)

(top - bottom)
Y = bottom + ------------------------------
1 + 10^(logEC50 - X)*hillslope


4. one site competition

(top - bottom)
Y = bottom + --------------------
1 + 10^(X - logEC50)

5. two site competition
fraction_1 1 - fraction_1
Y = bottom + (top - bottom) *( --------------------- + -------------------- )
1 + 10^(X-logEC50_1) 1 + 10^(X-logEC50_2)

and a few others:

6. boltzmann sigmoid

7. one phase exponential decay

8. two phase exponential decay

9. one phase exponential association

10. two phase exponential association

11. exponential growth

12. power series

13. polynomial equations

Cheers,

Dave

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