Suppose I dock 10 ligands to 5 different proteins. My goal is to say "find out the ligand with the best combination effect". I need my ligand to have maximum docking score against say Protein1 and lower docking scores against say Protein 2,3,4 and 5.
What techniques to can be used to predict the best possible ligand ??
Thanks in advance
hi,
i think, the best method is by using their binding energy. Lease the binding energy, higher the binding affinity.
Secondly, u need to check the positions where the ligand got binded if u are doing a blind docking. If the position is not at their active site, check for the next binding pose and consider the pose where the ligand binds to the required position in the protein.
docking scores
Ligand protein1 protein2 protein3 protein4 protein5
a -72.15388 -71.307 -67.1854 -69.4547 -67.9582
b -71.46606 -73.285 -77.9395 -76.0567 -70.1417
c -66.17677 -78.350 -70.4459 -69.9967 -72.4975
d -62.02596 -67.456 -58.2813 -69.5027 -69.7021
e -60.41975 -69.861 -57.5646 -73.3378 -71.6445
f -60.32962 -64.417 -51.9968 -67.197 -65.7883
Sir, the scores look like dis.... Now which one do u think is "the best" selective towards protein1 ??
That's the confusion... I can assume one based on binding affinity and docking to active site... however, is there any logical technique to find it out ??
It would be difficult to comparing of docking energy in different protein to get new better ligand
Pallab,
I suggest you a simple way. Find the difference in delG between protein 1 with respect to other proteins. Find only those ligands with more/better difference in delG with respect to individual proteins or a protein set.
This will only give you qualitative idea on binding of ligand. Its not wise to extrapolate it to selectivity. Extrapolating with homolog proteins is arguable but with non-homolog proteins is skeptical.
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