AMBER Archive (2009)
Subject: [AMBER] how to use amber to verify the reason for difference in affinity
From: Josmar R. da Rocha (bije_br_at_yahoo.com.br)
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?
Thanks in advance