Fragments for proteins with known structure for use in Rosetta

Question

[aa]

I would like to run some experiments using the basic monte-carlo algorithm in Rosetta, and compare the results to the real thing. However, I have no idea where to get the fragment files necessary for this. I've looked at a few fasta files from completed queries submitted to the Robetta server, but (not surprisingly) I haven't come across any short (>100 residues. Didn't bother looking at longer ones) with known structures.

I don't want to submit anything to the server because I'm not even sure I can, and, if it's possible, I'd rather not take up any of the server's time if I can get my hands on a few of there on my own.

I'd expect that (at least) the files mentioned in the example in D060_Folding.py would be there, but they aren't. I found a file of only 3-mers (used as an example for the workshop assigments), but no 9-mers.

Does anyone happen to know of any small proteins with known structure and available fragment files?

Answer 1

[Felix_Sim]

Submitting to the Robetta server is generally not a problem. You might be in the queue for a few hours but the submission restriction to a maximum of 2 at the same time will get your fragments to be generated quite quickly. Using the server for a protein of interest is really the easiest route in my opinion. The server stores your files for up to a week (if I remember right).

Your second option, if you are in academia, is to download and install the Rosetta package itself. You can generate 3- and 9-residue fragment libraries using the fragment_picker executable. However, it requires some computational power and the installation is not always the most straightforward.

Personally, I would advise you to choose a protein you are interested in, submit the sequence to the server and generate your own fragments. I find that the best way to learn and understand what is going on. The server will generate a number of files, such as a secondary structure prediction etc, but most importantly two files - the 3-residue and 9-residue fragment files.

Hope this helps.