[gmx-users] flexibility

[Tsjerk Wassenaar]

Hi,

The usual (statistical) way to compare fluctuations (variances) is by
taking the ratio (i.e. of the MSFs, not the RMSFs). Maragliano e.a.
(BiophysJ 2004) wrote on such comparison of fluctuations, using a
variance ratio test.
In your case, you'd have to combine it with a structure alignment to
find which numbers should be compared with which.

Cheers,

Tsjerk

On Wed, Jun 1, 2011 at 1:24 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
> --
> ========================================
>
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands