Thank you Emanuel. I will try what you have suggested and I think I will try to confirm it exeprimentally to be sure about my initial structure. This is terminal which is highly flexible and beta loops are very common for this sequence. Thanks a lot!
Steven On Mon, Jan 9, 2012 at 9:19 AM, Emanuel Peter < [email protected]> wrote: > Hi Steven, > > There is a difference between homology modelling and ab-initio modelling. > With SWISS-modeller or ITASSER you have a lot of templates, which are > searched > automatically. In case, if this part of the sequence does not have any > homology, > then your model contains loops and has no secondary-structure as > alpha-helices > or beta-sheets. > As one possibility you could model these parts by ab-initio modelling > (ROBETTA). > Another possibility could be the MODELLER. > From the bunch of models you should decide yourself, what's the most > reasonable one. > [ Radius of gyration (SAXS). Secondary structure prediction (SSPRED) ] > > I am not sure if this could help you further and of course I am not an > expert in > this field. I do not want to open a huge discussion with personal attacks > as it > is usually done in this list. > > Bests, > > Emanuel > > >>> Steven Neumann <[email protected]> 09.01.12 9.51 Uhr >>> > > Dear Gmx Users, > > I am wondering whether any of you faced a problem of predicting terminal > of the protein. I submitted my sequence to the software like ITASSER or > LOMETS and obtined some models forming loops which are expected. The > confidence of those models (as this is terminal) are not so high and I am > wondering whether I will confirm sencondary structure of my protein > exeprimentally (CD exepriment) I can trust and choose one of models formed > by the server? Please, let me know if you had similar problem in your past. > I am writing this message on this forum as many people are studiyng > proteins in Gromacs. If you can suggest other mailing list I would be > grateful. > > Thank you, > > Steven >
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