Hi everyone,
I would like to repeat and extend this study with PyRosetta, yet I am new to it. I have the PyRosetta tutorial book here in front of me and working through it.
How should I go about creating the fragment database? Manually select the fragments and go from there?
How can I re-create similar structures and expand from there?
Some general pointers would be great.
Thanks,
Thomas
Category:
Post Situation:
While picking fragments could theoretically be done through Python and PyRosetta, I don't think anyone has the wherewithal to actually do it. Instead (assuming you're an academic/non-profit user), I'd recommend just using the Robetta server and input the fragments as a file.
Past that, I'm not sure that anyone has put together this particular protocol in PyRosetta yet. Most of the pieces should be there, but actually finding them and putting them together in the right order may take a bit of hunting and leg work. If you have futher questions about how to accomplish any particular step, please let us know.
I agree.
I am one of the authors, and still working on repeat proteins after moving on. I am not using PyRosetta, but if you have specific questions about design, protocols and expansion, just get in touch.
Fabio