Dear amber users,
I would appreciate if someone could give a tip or to point some reference on how to use amber in my problem. I tested two very similar compounds against a protein and one of then is 500-fold more potent than the other. I guess that the diference is caused mainly due to a charge stabilization of a deprotonate cystein through the interaction with a diene fragment, which is replaced by a saturated fragment in the less potent compound.
1-How could I verify this hypothesis?
2-When I use MM, is this kind of effect is taken into account?
Thanks in advance
Josmar Rocha
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Received on Tue Nov 24 2009 - 14:30:03 PST
