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 <jalem...@vt.edu
<mailto:jalem...@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
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Bharat
Ph.D. Candidate
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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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