How much favourable is -6.78 delta G value for docking a ligand for an enzyme, please help me with this as it will help me intern to create in-silico evidence for a viral infection.
I believe there are no criteria for delta G.
it depends on your active site and your ligand.
I worked on a project and I analyzed the known inhibitor delta G was -3.7 which computationally can be considered poor an unfavourable but this inhibitor is better than two drugs performed -4.6 and -4.5.
again it depends on the active site and your ligand if your ligand fit inside the active site with no clashes or bump don't care about the delta G.
Hi
To estimate how favorable your score (delta G) is, you may compare it to the score of a known standard.
The "deltaG" reported by a docking software is in fact just a scoring function that gives a VERY ROUGH idea of how preferable a certain docking pose is. It is almost never equal to the actual experimental binding energy, and only some loose correlation can sometimes be found in a series of compounds. Small differences in the scoring values for different poses and compounds (up to 1-2 "kcal/mol") are meaningless. Some methods even don't use the energy units for it, avoiding this misunderstanding.
Docking, as is, cannot prove anything, it only provides some (inherently uncertain) hypotheses. Of course, if a compound cannot be docked at all, the chances for its binding are pretty slim, but most programs will dock almost anything in some way or another. If your goal is virtual screening, you should first test your docking procedure on large set of actives (known) and inactives (known or simulated using decoy approach). That way, you will be able to validate the model and determine a reasonable threshold. You must answer questions like: Does it actually differentiate actives and inactives? How well they are separated? What threshold is better in terms of false positives and false negatives? What are the accuracy parameters?
Of course, all that is impossible if you have only one compound. You can, however, thoroughly analyze the proposed binding mode (Does it look reasonable? What are the interactions? Does it match available X-ray data, mutation data, and other available information?). Also, you can dock known ligands and compare the results (but keep in mind that generally larger ligands will give better scoring even if the binding is actually the same or worse).
Finally, the binding stability and pose should be checked by molecular dynamics simulations.
Thank you all, it helped me finding a potent phytochemical drug.
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