I have a different weak point: my right knee. 

I work regularly to strenght it doing squats on a bosu ball and standing on the bosu ball on one leg while raising a dumbbell.

I'm pretty sure those exercises would also help strenghten the ankle. 

And shoes are key. I recently tried a new Broosk model and after a week I had to go back to the store and buy a pair of my regular model (Brooks Glycerin). 

 Have you tried running in barefoot shoes, like vibrams?