The Molecular Graphics Laboratory Forum

I docked some molecule to the same receptor using vina, show logarithmic relationship between the affinity and molecular mass. Can I compare the affinity of molecule with different molecular mass?

Hi cndenis,

Interesting observation and graph. I am relatively new to Vina myself, so the following may be of little help.
It makes a bit of intuitive sense that given a large area for potential binding, a larger molecule will have more chances for favorable interactions, summing to a higher absolute binding affinity.
A way to avoid this phenomenon may be to carefully select (ie, minimize) your search space on the receptor to include just the active site cavity, so that large ligands will not have an "advantage."
If you try the above and the trend is still present, a practical solution, which could apply to an application such as virtual screening (which may apply since you seem to be looking at several ligands), may be to take your absolute highest binding affinity molecules as potential hits, but then also select as "hits" some lower value small molecules that have affinities significantly larger than predicted by your mw vs. affinity curve.

Seth