RFpeptides

[wangzaimieyoutou]

I have been trying to follow the code examples in the README and also attempting to use design_macrocyclic_binder.sh for Macrocyclic peptide design with RFpeptides, but the output doesn't seem to form a cyclic structure as expected. Should I increase the number of designs generated to improve the probability of forming a cyclic structure?

[roccomoretti]

When you say it doesn't form a cyclic structure, how are you checking? How far off of cyclic is it?

Note that "cartoon" representations in structure viewers like PyMOL and ChimeraX tend not to do well with cyclic peptides, and may show a cartoon with a noticeable gap. Try turning off the cartoon representation, and use a "sticks" style representation (one which shows the actual atoms and bonds). It may be that your peptide closure geometry is fine, despite it looking broken when it initially loads.

[DazLe-Q]

Hi, related to this topic, I have a question: Does the size (number of amino acids) of a designed peptide affect the cyclization of the model? Because when I set an exact size of 11 aa, the results are entirely in the form of straight-chain alpha helix.

[wangzaimieyoutou]

I used Maestro and PyMOL to check its structure, and based on the results, it doesn't seem to be the issue. Also, I have the same problem as DazLe-Q—after increasing the number of amino acids, the results are entirely in the form of a straight-chain alpha helix. Below are my results.