[gmx-users] Help: Analysis large interdomain motion

T.A.Wassenaar T.A.Wassenaar at rug.nl
Tue Apr 19 14:23:33 CEST 2005

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.



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 
> 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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