I am trying to do homology modeling. I thread around a thousand structures. Before performing the energy minimization, I want to identify broken structures and stitch them. What are the possible ways to do it? So basically,
1. I want to identify those structures that require loop modeling (broken structures)
2. Perform loop modeling on all those (say there are a couple of hundred structures).
3. Then perform energy minimization.
I looked at the loop modeling algorithm. It requires a loop file. But, how I create so many loop files? Is there a simpler way that says, look at the native, identify places where the target is broken and fix it by putting fragments from the native pdb?