[gmx-users] Protein Structure Prediction

[Steven Neumann]

Hi,

Thank you! So what kind of exepriments will you suggest? Is CD enough? I
can also perform Microcalirometry for secondary structure.
The one chain (N terminal) is 180 amino acids and second (C terminal) is
150. They have similar sequence as they are polyglycine peptides which are
known to form loops (beta loops).

Steven

On Mon, Jan 9, 2012 at 9:52 AM, Thomas Evangelidis <tevang3 at gmail.com>wrote:

> Hi,
>
> The problem with I-TASSER is that you cannot use the desired templates for
> threading. The server has an option to exclude specific templates but it
> will always find distant "homologues" to use to create restraints and
> fragments. ROBETTA has also the same disantvantage. I would recommend using
> standalone programs like Rosetta (for ab inition structure prediction or
> homology modeling), MODELLER (homology modeling), etc. Also collect as many
> experimental data as possible and use them as restraints during modeling.
> Termini are very flexible and structure prediction is very chalenging for
> these parts.
>
> By the way, what is the length of the missing part?
>
> Thomas
>
>
>
>
> On 9 January 2012 11:29, Steven Neumann <s.neumann08 at gmail.com> wrote:
>
>> 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 <
>> 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
>>> (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
>>>
>>>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
>
> Biomedical Research Foundation, Academy of Athens
>
> 4 Soranou Ephessiou , 115 27 Athens, Greece
>
> email: tevang at bioacademy.gr
>
>           tevang3 at gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
>
>
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