We have used CaFE Software to predict the binding free energy of our protein-ligand complexes from our molecular dynamics simulations.
Fortunately the Software has run successfully however don’t know the exact meaning of the physical thermodynamic parameters calculated: a) Complex total (kcal/mol), b) Receptor (kcal/mol), c) Ligand (kcal/mol) and d) Delta (kcal/mol).
We understand that the first value “Complex” can be interpreted as the binding free of the protein-ligand complex , However, we are bit confused about the last two terms “Ligand” (c) and Delta (d) what would be the difference between them? or which is the most important parameter to determine the binding free energy of the ligand to the receptor, is that (c) or (d) parameter?
Thanks in advance and best regards,
Dear Marlet Martínez-Archundia,
I assume you are calculating a difference in energies of some kind, possibly a difference between final and initial states (seems like an end-point "free energy"). So, you could summarize your system this way (one of the most elementary assumptions):
R + L --> RL (Where R is the receptor, L is a ligand, and RL is a complex formed by the non-covalent interactions between the receptor and the ligand). Same as:
Initial --> Final
And you want to calculate the energy difference between your "free" receptor and ligands and your "complexed" receptor and ligand, so those "energies" are:
E(R) + E(L) = E(RL)
Since talking about "energies" makes sense if you compare it to a reference, then your interest at the end of the day, is the difference between the final and initial states, which is the "delta" you mention:
delta(E)= E(RL) - [E(R) + E(L)]
How you define these "energies" and what interpretation you give to the difference between the two states is a question specific to your computational method and what you are investigating.
I hope I have helped you,
Bests,
Dear Edward Francisco Méndez Otálvaro , thanks a lot for your kind response. I think it does make sense in that way,
Best wishes
Marlet
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