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Can loops be modeled in Homology Modeling and then inserted in an existing structure in CAD?

Last Updated: Nov 01, 2017 11:15AM PDT
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.
 
  1. Insert desired loop sequences into your FASTA sequence, then run in Homology as a structure prediction.
     
  2. Load the resulting structure into CAD.
     
  3. 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.
     
  4. If not,  you may run 1 --> 2 --> 2a with some sequence ideas until you get a loop structure that looks right.
     
  5. Run one or two cycles of Design/Minimize (e.g. Design/Minimize/Design/Minimize) on the loop alone, or the loop and its neighbors.
     
  6. Test the final loop with Relax again to make sure it does not fall apart.
     
  7. 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.
 
ef828e56a55e7b26e25ee456cc7df695@cyrusbiotechnology.desk-mail.com
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