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[NickJ]

In pondering the excesses inherent in most Markush representations of drug like molecules I was wondering if there were computer programs developed which create those endless series of side-chains.

I mean, I find it hard to envision the molecular spaces carved out by such entities. The common elements, besides the elements themselves, is often tenuous at best.

Or does the rationale reside in the agent saying "that looks scary enough to ward off any infringers"?

I've heard of MARPAT but am not sure it can catch complex cases.

[pentazole]

Well...  drug like molecules or not so drug like, the side group language is going to be extensive.  Usually a molecule has an active site, or an active group, or an active core, or whatever, and everything else is (more or less) irrelevant.  The last thing you want is to discover a molecule that's useful for something, and have someone use a side group that contains a nitrogen for example, instead of the sulfur that you originally had, and get around your patent.  

So as an agent drafting a patent, you are going to throw in there as much as you can to give as much protection as you can for your client, but in the end, a molecule is defined by certain properties, and these side groups that you are adding are under the assumption that they do not drastically change the properties of the molecule.

When someone else comes along and makes a similar molecule that has a side chain that you listed as part of your side group possibilities, but in this case, the molecule exhibits properties different from what you had disclosed, then that someone has a case for unobviousness...  and all is good.  There's plenty of case law out there regarding homologs and such.