We have used FRET method to see the donor(protein)- acceptor(drug) distance which we get for our system as r=1.6 nm. Docking we perform to find out binding site of that particular drug in protein and the nearby amino acids. can we correlate this two techniques any point of view? is r=1.6 nm consisting with our docking result.
Any comments/help is most welcome !!!
FRET is called the spectroscopic ruler. It should correlate with the docking result. However, some things are needed to be considered such as: donor here is not the protein but the fluorophore moiety/moieties present in the protein. If there is only one trp in the protein (and no tyrosine) then the distance from the center of mass of that trp ring system to the center of mass of the ligand ring system, should be considered. If there are more fluorophores, average distance from all these fluorophores needs to be computed.
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