On Fri, Apr 10, 2009 at 12:29 AM, Claudia Scotti <[email protected]>wrote:
> I'm trying to model the 20 residues-long single transmemebrane domain of a > protein and it is recognised, as expected, to be an alpha-helix by several > programs. Homology modelling fails for lack of sequence similarity and > modelling by the HMMSTr-Rosetta models it as a beta-sheet. > > Please, would anyone have any suggestions on how to proceed or might please > someone indicate a more appropriate forum/list for modelling problems? > Perhaps I'm missing the point, but couldn't you just take an ideal helix of appropriate length and mutate the sidechains in Coot or PyMOL to match your sequence? If you're concerned about realism you could run energy minimization or even quick MD. Unless you have prolines or glycines in the middle of the helix this is unlikely to be much worse than a remote homology model. (It depends on what you plan to use the model for, of course - I've only done this for making figures.) Alternately, if you have Modeller, there is this: http://salilab.org/modeller/wiki/Make%20alpha%20helix -Nat
