[gmx-users] flexibility

[Justin A. Lemkul]

shiva birgani wrote:
> 
>     Message: 1
>     Date: Tue, 31 May 2011 06:56:16 -0400
>     From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>     Subject: Re: [gmx-users] flexiblity
>     To: Discussion list for GROMACS users <gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>>
>     Message-ID: <4DE4C950.70704 at vt.edu <mailto:4DE4C950.70704 at vt.edu>>
>     Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> 
>     shiva birgani wrote:
>      > Dear all
>      > I have simulated two different proteins (A and B). I need to compare
>      > their flexibility. RMSF help to examine their flexibilty
>     individually,
>      > but I want to campare them with each other.
>      > Do anybody know a solution to this? Would you please help me in
>     this regard?
>      >
> 
>     Is it not just a matter of comparing the RMSF between the two proteins?
> 
>     -Justin
> 
>     --
>     ========================================
> 
> Dear Justin
> 
> Yes I want to compare them, but I am not sure that RMSF is appropriate 
> test to comparison, because two proteins are completely different in 
> their amino acid contents and numbers.
> 

RMSF is the correct metric for measuring the flexibility of your proteins.  How 
you then interpret the data in light of what's known about your system and the 
goals of your study is up to you.  All part of good experimental design.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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