Dear Researchers and Professors, recently I faced some doubt in molecular docking energy result. Herewith I have enclosed CDOCKER (Discovery studio software) energy values of some docked molecule. Generally in literature mentioned, negative docking energy values indicates more binding energy. In following attached image which molecule has more higher binding interactions? Kindly explain. My doubt is in the result table commonly mentioned (-CDOCKER energy). Means the all the positive values are considered as a negative value or not?. Some time the values shows in negative values.
Hello Bala Subramaniyan
In CDOCKER Discovery Studio software the scoring function and binding energy terms are different than other software scoring function.In these software the CDOCKER score(interaction energy) is good if the docking value in positive. The more positive, the more favorable interaction. In other , the binding energy term(binding energy) , the more negative value, they have better binding affinity.
But in terms of Autodocktool,the scoring function differs,the more Negativity of the interaction,the stronger the Binding energy and the interactions.the more negative value,the stabler the compound or affinity.
Energy scores in the docking process are various. you should read the detailed manual of cdocker. for the score, generally positive and highest prices are chosen for the best poses for docking results.
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