No, there is no way to use such data to determine the folding rate of
the intact protein. If you used a fragment approach you could
potentially (read lots of papers on REMD) isolate nucleation sites,
but minus the tertiary interaction scheme you could not tell a
compelling story. Now, if you want to find nucleation sites and see if
there are spatially proximal sites and simulate them together... You
might begin to tell a story.
Ken
On Dec 30, 2011, at 6:09 PM, Justin A. Lemkul wrote:
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
-- ==============================__==========
Justin A. Lemkul
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Virginia Tech
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Bharat
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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
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