Dear Modeller users,
I have a protein, its full sequence and most part of its structure have been known, except 4 segments of loops (6-15 residues long). Can I use modeller package to add the loops to the known core of the protein? How? Where should I begin from?
I know that I definitely should delve into the tutorial or manual first, try different things and then ask question here. However I just heard this modeling package minutes ago, and just registered, downloaded, and installed it. I am in a rush to get the last step of my current project done. Hope somebody can give me some hints.
Thank you very very much!
Cheers, Mingfeng Yang
Mingfeng Yang wrote: > I have a protein, its full sequence and most part of its structure have > been known, except 4 segments of loops (6-15 residues long). Can I use > modeller package to add the loops to the known core of the protein? How? > Where should I begin from?
This is very similar to the 'missing residues' problem that comes up occasionally. There is an example of how to add such missing parts of a structure, knowing its full sequence, in the Modeller wiki at http://salilab.org/modeller/wiki/File_archive (go to 'Missing residues').
You will probably have trouble building reasonable-looking loops if they are 15 residues long; sampling of the conformational space becomes an issue. For these longer loops, you should try to find other templates or impose suitable restraints (e.g. secondary structure if you know it).
P.S. Other users can add their own examples to the wiki pages, of course.
Ben Webb, Modeller Caretaker
participants (2)
-
Mingfeng Yang -
Modeller Caretaker