[gmx-users] Re: Folding rate

[Justin A. Lemkul]

bharat gupta wrote:
> Thanks for your reply. I want to whether does it make any sense or is it 
> possible to simulate fragments of proteins and find their folding rate 
> and then correlate it to folding rate of whole protein ??
> 

Simulating arbitrary parts of a protein may or may not produce any relevant 
information, likely the latter.  Independently folding domains might be 
simulated in isolation, but if there is a chance that the peptide sequences have 
any effect on neighboring residues or even more distal sites, you'll never 
produce anything useful.

-Justin

> On Sat, Dec 31, 2011 at 8:00 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     bharat gupta wrote:
> 
>         Hi,
> 
>         I want to know whether it's possible to calculate the folding
>         rate of 20 residue peptide folding into a beta-hairpin using
>         gromacs ??
> 
> 
>     Anything is possible ;)  But seriously, there is existing literature
>     on such topics, I suspect you can find methodology that will suit
>     your needs.
> 
>     -Justin
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
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> -- 
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
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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

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