How are number of interactions, types of interactions, and angstom of each bonding effected binding energy(be)?
Many articles said something like the more the interactions the lower the be. But i found it very confusing when i inspect the ligand-protein complex interactions one by one. For some, the more the interactions, yes, the lower the be, but for some it is not like that.
A docking algorithm-specific empirical scoring function returns a docking score, usually an arbitrary number with a fancy name attached to it: binding energy, binding affinity, etc.
These are just empirical, for comparative purposes within, and have no relationship with the actual energies.
the type of bond that exists is to determine the docking score (Gibbs free energy, affinity, binding energy). Types of bonds in organic molecules include covalent bonds, including hydrogen bonds and other hydrophobic bonds. These bonds are considered in molecular docking.
Hello Marko Jeremia Kalalo
Actually, we can't claim a docking a good/bad docking only by analyzing the global binding energy of docking ( docking score).
There are some other factors like IC50 value of the ligand, size of ligand, molecular simulation, size docking pocket, presence/absence of allosteric side, ligand binding to the pocket or not, interaction residue.
For example, if you find a docking score of -100 KJ, it can be a good/best docking score. Still, if the 3D position of the ligand tels that the ligand does not reside in the binding pocket well or the IC50 value of the ligand is not that good or the binding interaction residues are histidine-excluding then the docking is not satisfactory, does not matter how big the docking score is!
Best Regards
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