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2c:
Back in the day, when I was using structures to design small tight
binding ligands, I found it really helpful when multiple superimposed
structures were available, typically from some dynamic simulation of
the protein, NMR structure or perhaps multiple Brookhaven PDB
structures suitably aligned. I really can't say for sure whether the
structures derived from dynamic simulations were necessarily
predictive (especially without NMR constraints) or the alignments
necessarily correct, but it was much easier to visualize disordered
regions vs. fairly ordered regions when presented with a ordered
collection of superimposed structures. This gave me information
about what sort of "flex room" was available in the active site,
which might give me the courage to explore new ligand backbones that
potentially might be larger but easier to synthesize, or might give
me some insight when expected interactions empirically didn't seem to
be there when you go to binding studies in vitro.
Anyway, I don't think it is necessary to present the user with just
one structure.
Ian
