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Disclaimer: Statistics is not exactly something I am particularly good at. So if this is a stupid question, I do apologize

I have been using non-linear regression to analyze binding between two biomolecules. Each individual experiment was done in triplicate. The average of these triplicate values (with associated error) were analyzed using regression ([L]=known).

Specific binding = Bmax*[L]/(Kd+[L])

The Bmax and Kd are calculated. Both values have 95% confidence intervals and standard errors reported.

I would like to compare the Kd for different pairs of Biomolecules. I.e. I would like to compare the Kd (higher or lower) for A binding to B, A binding to C and A binding to D. In addition, I would like to compare binding between AB and XY. Which test(s) would be appropriate for this analysis?
Any suggestions would be greatly appreciated!!

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up vote 1 down vote accepted

To compare bindings, you want to do an ANOVA where your dependent variable is specific binding and your treatment is type of molecule. If the p value for the ANOVA is less than 0.05, the type of molecule does influence the specific binding. Then do a multiple comparison test (such as Tukey's test) to see which specific bindings are different. What software are you using? I can explain further if necessary.

To compare Bmax and Kd, you can look at your confidence intervals for each type of molecule - if the 95% CIs don't overlap, the two coefficients are significantly different at the 5% level. (note that this type of test ignores the multiple comparison problem)

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I am using graphpad prism. Tukey is easily implemented using this program. – Stylize Oct 3 '12 at 14:29

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