In Autodock Vina, parameter of binding energy has been used to determine which ligand that has stable complex interaction with protein (e.g enzyme). And more negative value or lower binding affinity, the more stable ligand-receptor we get. What parameters that can be make binding energy have more negative value? E.g more interacting with the pockets of protein, the more lower binding energy we get. Any suggestion can be help. Thank you
Empirical methods such as docking usually use scoring function to measure the likelihood of ligand to bind to the protein target. Autodock vina uses several terms to be included in its own scoring function: gaussian, repulsion, hydrophobic, hydrogen bonding, and the number of rotatable bonds. Details can be found in its paper section methods--> scoring function
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Saipul Maulana The interaction of most ligands with their binding sites can be characterized in terms of a binding affinity. In general, high-affinity ligand binding results from greater intermolecular force between the ligand and its receptor while low-affinity ligand binding involves less intermolecular force between the ligand and its receptor. The lower the Ki concentration is, the more likely there will be a chemical reaction between the pending ion and the receptive antigen. Low-affinity binding (high Ki level) implies that a relatively high concentration of a ligand is required before the binding site is maximally occupied and the maximum physiological response to the ligand is achieved.
You should also consider the type of inhibition you are looking for, since very large and negative values accompanied by strong electrostatic interactions can lead to suicide inhibitors or covenant inhibitors, which is not so good when you are looking for a pharmacologically interesting compound.
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