I've got a 20 aa loop and I am wondering will the Loop refinement
protocol in Modeller can handle such big loop? Is there any parameters
can be refined to get more reliable model for such big loop?
Modeller will model a loop of any length, but the longer the loop, the
larger the conformational space that needs to be explored and so the
less likely you are to sample the global minimum. As a general rule of
thumb, the longer your loop, the more models you need to build to sample
the space. For example, the ModLoop web server builds 300 models and
works reasonably well for short loops (maybe up to 8 or 12 residues).
For 20 aa loop, you'd have to build many more models.