Cyrus Bench Loop Rebuild is currently in Beta testing. However, the method you propose is great and routinely used to do loop extensions. Here is a suggested workflow.
- Insert desired loop sequences into your FASTA sequence, then run in Homology as a structure prediction.
- Load the resulting structure into CAD.
- Optionally, you can "test" a structure by running some Relax (say 5 runs) to see if the new loop is stable. If it is, that's a great sign.
- If not, you may run 1 --> 2 --> 2a with some sequence ideas until you get a loop structure that looks right.
- Run one or two cycles of Design/Minimize (e.g. Design/Minimize/Design/Minimize) on the loop alone, or the loop and its neighbors.
- Test the final loop with Relax again to make sure it does not fall apart.
- This can be done iteratively, e.g. go up to 3, then take that design sequence back to step 1, and look for convergence of designed sequence to intended structure.
A "good" new loop is one that has a sequence/structure combo that is stable to Relax.