I'm comparing my top1 ligand in docking and my reference ligand. My reference ligand has more strong interactions than my top1 ligand but my reference ligand has a less negative binding energy than my top1 ligand.
Theoretically it should be the opposite right because complex with stronger interactions should have more negative binding energy. But the actual results are different.
What is the explanation for this? Is there something that I'm missing out to study?
On what basis you are saying strong interactions????
Binding energy is derived based on the bond formations between the ligand and protein binding moiety.
Higher no. of hydrogen bond in a ligand does not mean that it will have more negative energy values. If other ligand have hydrophobic interactions and other bonds comparatively more than that of H bonds, then these hydrophobic interactions can compensate the energy of binding.
Therefore, I suggest you to look into others interactions also.
Check the docking score on the basis of that you can conclude the strong binding interaction between ligand and refrence.
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Computer Graphics and Animation
- 3D