[gmx-users] Protein Structure Prediction

[Thomas Evangelidis]

Also consider Raman and FT-IR spectroscopy as well as the results form
consensus secondary prediction servers and biological information in the
literature to assign secondary structure restraints to specific residues.
This task requires a lot of biophysical intuition so I cannot help you
further in this regard.

Thomas


On 9 January 2012 12:37, Steven Neumann <s.neumann08 at gmail.com> wrote:

> 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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>
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-- 

======================================================================

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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