I have been working with molecular docking for a while.
Til now, I always be lucky enough to get the structures from Protein Data Bank :)
Now, I am working with some proteins (from fungi) that there aren't X-Ray structures. So, I search for a reliable tool to predict structures and found Phyre.
In my first job (42b752f1abbc2514), the alignment covering is 21% whereas the confidence is 96% and the percentage identity is 17%.
My doubt: what criterion should I use to select a model and use it in my docking studies?