[kinda_concise]

Pharmacologist, looking in to the ability of a drug to activate intracellular signalling. I've classified my drugs in to two groups, ability to activate or ability to inhibit ERK signalling. I'm interested in finding the structures common to one group and not the other. What's the best way to do this?

[pgk]

You get the principal or principal molecules of the group of interest, then  “isolate" the pharmacophoric group  and try to correlate  and simulate possible chemical structures, taking in account, mainly, the MW and lopgP limits of the receptor and any possible isosterim. If you have access to a specific software, your life will be easier.
Of course and meanwhile, you search in the corresponding literature, too.

[kinda_concise]

I'm still searching the literature with little luck. What is the specific software?

Thanks for the help.

[pgk]

Please, take a look to the link bellow, in order to get an idea.
http://www.click2drug.org/
Among them, the free version of ACD/ChemSketch has a tool for the calculation of logP.
http://www.acdlabs.com/resources/freeware/chemsketch/
Also, take care to the correct stereochemistry of the molecules.