[gmx-users] Help: Analysis large interdomain motion

[Oliver Beckstein]

Adding to the discussion on NMA, protein motions, visualisation and such:

A colleague of mine, Dr Paul Barrett, set up a web service called
'Dynamite' at

 	http://dynamite.biop.ox.ac.uk/dynamite

Amongst other things, it produces PCA of protein ensembles based on Bert
de Groot's CONCOORD and visualises them nicely as 'porcupine plots' (the
arrows sticking out from the backbone).

You can also analyse xtc trajectories of your own.

Have a look at the site, read the available documentation, and contact
Paul (address on the website) if there are any further questions.

Best wishes,
Oliver

On Tue, 19 Apr 2005, T.A.Wassenaar wrote:

>
> Hi Zhenting Gao,
>
> Actually, this is not uncommon. The analysis you probably want to perform
> here includes principal components analysis and subsequently running the
> program DynDom to reveal the nature of interdomain motions. From what you
> mention you might also be interested in visualization of the loadings of the
> principal components, though that has not been added to gromacs yet.
>
> Cheers,
>
> Tsjerk
>
> On Tue, 19 Apr 2005 19:44:23 +0800
> "Zhenting Gao" <zhentg at 163.com> wrote:
>> Hi  gmx-users ,
>> I am currently working on a protein with 3 domains: left, middle and right
>> domain.
>> While the 3 domains' internal structure remain almost unchanged(rmsd of
>> each domain is below 2.5A if fit to itself), the interdomain motion between
>> the left and right domains are comparably large, i.e. the rmsd of right
>> domain is more than 12A if fit to the hydrolase domain.
>>
>> Does anyone know a protein like this? As I concern mostly at the residues
>> which are indispensable for the large interdomain motion, what can I do to
>> persue this?
>>
>> Any suggestion or papers are heartily appreciated.
>>
>> Yours sincerely,   Zhenting Gao   zhentg at 163.com    2005-4-19
>> ------------------------------------   Drug Discovery and Design Center,
>> Shanghai Institute of Materia Medica,   Chinese Academy of Science
>> P.R.China   http://www.dddc.ac.cn/group/zhentg.htm
>>
>>
>>
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--
Oliver Beckstein * oliver at biop.ox.ac.uk
  http://sansom.biop.ox.ac.uk/oliver/