When the binding energy value obtained in molecular docking studies is positive, is it possible for the ligand/substrate to dock into the protein? How does the docking process occur when the Gibbs energy change is positive since the event is involuntary. Can somebody possibly explain this situation?
Dear Bahri.
Unfortunately, your question is not corroborated by important information.
I premise that in silico-docking, with molecules modeled in silico, and not by molecular dynamics in a water cage, has no significance. We can have errors of 100%. Traditional static docking simulations suffer from strong limitations, related to the treatment of ligands and targets. They neglect solvation and entropic effects, strongly limiting the predictive power. In the last years, methods based on molecular dynamics (MD) have emerged for simulating macromolecular complexes. The major problem of docking are the water molecules. The problem is that water molecules plays an important role in the accuracy of ligand − protein docking predictions. In fact, crystal structures contain water molecules in their binding sites and water molecules in the immediate vicinity of both the ligand and the protein have to be considered for a reliable and effective binding. The overall increase in accuracy when water molecules are included during docking simulations is significant and is independent from the method of optimization of the orientation of water molecules.
What did you use and how did you dock? Ask yourself this question first, then talk about free energy.
Greetings
Docking score is not protein-ligand binding free energy. Protein-ligand binding free energy is an ensemble property. Protein-ligand binding event is a solvent substitution event.
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