[gmx-users] Re: Folding rate

[bharat gupta]

Thanks for your advice... Could you please refer me some papers regarding
this ....

On Sat, Dec 31, 2011 at 8:17 AM, KS Rotondi <ksr at chemistry.umass.edu> wrote:

> 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 <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://vt.edu/Pages/Personal/justin>
>>>   <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
>>> Biomolecular Engineering Laboratory
>>> Division of Chemical Engineering and Polymer Science
>>> Pusan National University
>>> Busan -609735
>>> South Korea
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>>> Mobile no. - 010-5818-3680
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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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
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-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
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