[gmx-users] Fwd: Simulation of protein with phosphate ion...
bharat.85.monu at gmail.com
Tue May 31 10:38:05 CEST 2011
Ya , I have tried with this server, but I am getting those residues whose
side chains are present inside the barrel. Then in no way phosphate ion can
bind to the barrel, as per the protein design rules..
On Tue, May 31, 2011 at 1:33 AM, Francesco Oteri
<francesco.oteri at gmail.com>wrote:
> Dear bharat,
> you can try Phosfinder (http://phosfinder.bio.uniroma2.it). It is a
> website that predict phosphate binding site on protein stucture.
> The paper url is: http://www.ncbi.nlm.nih.gov/pubmed/21622655
> Il 31/05/2011 02:06, bharat gupta ha scritto:
> thanks ...
> On Mon, May 30, 2011 at 5:03 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>> bharat gupta wrote:
>>> Well, mine is a beta-barrel protein called Green Fluorescent Protein. In
>>> such a case the movement of ion is very important. As the ion in side the
>>> barrel can quench the fluorescence. That's what I want to track..
>> You can probably address this with the methods I've described. That's
>> likely all that anyone can offer. Spend some time looking through the
>> literature at the many kinds of systems that have been addressed using SMD
>> and/or umbrella sampling and come up with a coherent plan to address your
>> system based on what you find.
>> 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
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