For a drug (suppose X) the thermodynamic parameters for BSA-X system from fluorescence method was found to be hydrogen bonding and van der waals forces while for the Lysozyme-X system the forces from docking method (by using autodock vina and discovery studio) we got as hydrophobic and van der waals. What may be the possible reason for this difference? is it due to two different techniques/ different proteins used? or water play a role as in docking we remove water while it is include in fluorescence technique?
A drug can interact with different protein in different ways due different physical and chemical nature of the protein. In order to corelate the fluorescence and docking results you need to keep the same set of protein and drug.
Dear Samina,
a bit more addition to the above-mentioned answers.
See, whatever the docking programs evaluate, it is just the most probable (optimized) ground state (global minima), whereas the fluorescence property doesn't correspond to it, it would rather correspond to the excited state.
Still, i anticipate that the trend should not changes if you have a series of such compounds. Further, i suggest you to not to focus on the absolute energies rather focus on the binding orientation (interactions) and geometrical features.
hope it helps
regards
athar
You are cent percent right. Amit has given you a right justification.
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