[gmx-users] Protein Structure Prediction

Steven Neumann s.neumann08 at gmail.com
Mon Jan 9 10:29:34 CET 2012

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!


On Mon, Jan 9, 2012 at 9:19 AM, Emanuel Peter <
Emanuel.Peter at chemie.uni-regensburg.de> 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
> 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 <s.neumann08 at gmail.com> 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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