Antw: [gmx-users] Protein Structure Prediction

Emanuel Peter Emanuel.Peter at
Mon Jan 9 10:19:41 CET 2012

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. 



>>> Steven Neumann <s.neumann08 at> 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,
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