I'm not sure if this the best place to ask, but I couldn't think of anywhere better:
I read and was really impressed by the conclusions of Koga, et al. "Principles for designing ideal protein structures". One thing that really intrigued me was the step in the process described as filtering for "local sequence structure comparability". Neither the article nor the example code seem to indicate how this filtering was done. The example RosettaScripts code simply indicates
## The filter for local sequence structure compatibility was done without using RosettaScripts
Can someone here provide a lead for how this step was done?
Not having read the paper, I have a feeling it's referring to Nobu's Rules. I think you need to ask him directly. I sent his email address to the email account you used to register for the forums.
Nevermind, I'm completely oblivious. It's clearly described in the Methods. I'm glad I caught this before I sent out the email.
Local sequence–structure compatibility
To evaluate the compatibility between the local sequence and the local structure, we collected 200 fragments for each nine-residue frame in the designed sequence from a non-redundant set of X-ray structures based on the sequence similarity and secondary structure prediction22 (the standard Rosetta fragment generation protocol for ab initio structure prediction). Then, for each frame, we calculated the root mean squared deviation between the designed local structure and each of the 200 fragments. Designs were ranked on the basis of the total number of fragments for which the root mean squared deviation was less than 1.0 Å, and those with high values were selected.