Aye, that's what got me thinking. Look at "rational drug design" where one selects various candidate substrates for high scores on binding to the active site of an enzyme...
By definition you have any number of candidates which bind more or less tightly to the site, some better than others.
In a biologically active system, one may attempting to tie up the active site of an enzyme with the drug molecule in order to prevent the enzyme from acting upon its 'naturally occuring' target; and of course there are other effects such as the drug interfering in other places, etc...
The analogy to protein construction (and even to building DNA) is that while the "proper" match is energetically favorable (the high score in the docking), there is nothing to forbid a different base pair, or amino acid from arriving first.
[Many deeper thoughts and pretentious drivel deleted...but available upon request.]
Cheers!
"The analogy to protein construction (and even to building DNA) is that while the "proper" match is energetically favorable (the high score in the docking), there is nothing to forbid a different base pair, or amino acid from arriving first."
No, but there are bouncers around to make sure they don't cause trouble.
As far as drug design, sometimes they have to bind more strongly and sometimes you can just overwhelm the natural substrate equilibrium with high drug concentrations. It's probably best to not bind a drug irreversibly - that screws things up for a long time.