A novel approach to determine docking locations using fuzzy logic and shape determination

The determination of whether a molecule can bind or ”dock” a protein to a certain site depends on the orientation of the molecules, the charge of the atoms that comprise the molecules, and the electrical potential of the proposed area. It is said that a fundamental problem with molecular docking is that the orientation space itself is very large and grows in a combinatorial manner with the number of degrees of freedom of the interacting molecules. We tried to cleverly solve this problem by using shape definitions and fuzzy logic to help reduce the search size of possible docking locations and predict which locations and orientations are the most likely docking locations.