A molecule shows the -11.6 kcal/mol and second one -8.0 kcal/mol so why molecule (A) revealed higher binding score. Please explain major factor involve in it.
The main factor involved in achieving a higher binding score in molecular docking is the strength and quality of interactions (hydrogen bonds, hydrophobic interactions, electrostatic interactions, and van der Waals forces) between the ligand and the receptor.
Shivangee Dubey
Thanks to reply, but the ligand is showing no interactions that hydrophobic totally. so any reason behind it? why is it showing higher binding energy?
The main factor of having a high binding score of ligand toward receptor protein is the position of the ligand in the active site, how well it fits into the active site, and also the different interactions (hydrogen bonds, hydrophobic, etc.), having stronger interaction will have high binding score.
Kavita Patel
but the ligand is showing no interactions that hydrophobic totally. so any reason behind it? why is it showing higher binding energy?
Does it having no Hydrogen Bonds, too? If it's having no interactions, neither hydrogen bond nor any other interactions, then check the structure of your ligand. Is it in 2D form?
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