I have performed docking analysis between a toxin( small chemical molecule) and it's nanobody. Does anyone have expirence in analyzing the results, i got some reaction sites and possible interactions, how can I understand which interaction is more possible? Just any experienced advice would be highly appreciated.
Docking programs generally give a score, which is a (not very accurate) measure of the strength of the predicted interaction. A higher score (or a larger negative score, in some cases) indicates a stronger predicted binding. However, you should not take docking results too seriously. Experimental verification is essential.
Do look for the interactions among the ligand and protein in Discovery Studio (Hydrogen bonds, hydrophobic interactions, electrostatic interactions etc.)....... a more negative binding energy is preferres as a good ligand (kcal/mol)...... Do check out the stability of the ligand through molecular dynamic simulations....
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