<html><head></head><body bgcolor="#FFFFFF"><div>Check Phys Rev Let 96 (2006) art nr 238102. You need simulations with reproducible folding so small peptides only. <br><br>Tot Ziens!<div><div><br></div></div></div><div><br>Op 4 jan 2012 om 02:35 heeft bharat gupta <<a href="mailto:bharat.85.monu@gmail.com">bharat.85.monu@gmail.com</a>> het volgende geschreven:<br><br></div><div></div><blockquote type="cite"><div>Thanks for all your replies. I want to know this can be done in gromacs or not - using REMD with structure based models generated from SMOG server to study protein folding and unfolding ??. Also, I have a question about how to determine the exchange probablities for a particular REMD experiment and also how many replicas do we need to consider, does that depend on the temperature list generated from the T_REMD server??<br>
<br><div class="gmail_quote">On Sat, Dec 31, 2011 at 11:36 AM, <a href="mailto:felmerino@uchile.cl">felmerino@uchile.cl</a> <span dir="ltr"><<a href="mailto:felmerino@uchile.cl">felmerino@uchile.cl</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p>Yeah sure. There are several methods to trick your peptide to fold, but often you loose the real kinetics by using them. I think a 230 residues protein is too big to study folding kinetics through MD (because of the folding kinetics, not the size of the system). With topology based potenitials (Go-like models) you surely can do it, but take into account the the core asumption there is that the energy landscape of your peptide is perfectly funneled to the native state, which is a very good approximation for small protein (like a 100 residues) but not so nice for bigger proteins. In fact, even small proteins have intermediate states which makes the energy landscape somehow rugged (the engrailed homeodomain, the trp repressor, etc). Besides that, it is not a trivial task to go from the reduced representation to real kinetic constants. Maybe if you are interested in comparison rather than absolute values you can be lucky with the Go-modeling. If that is the case maybe you should try the SMOG potential.... it is very fast.</p>
<p> </p>
<p>regards</p>
<blockquote>----Mensaje original----<br> De: <a href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a><br> Fecha: 30-dic-2011 22:45<div><div class="h5"><br> Para: "Discussion list for GROMACS users"<<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Asunto: Re: [gmx-users] Re: Folding rate<br> <br> The protein that I am dealing with is a 230 amino acid protein. I have come across some methods that used reduced space model of protein such as CABS for locating the protein folding pathway. An another paper describes about using Go model together with Rigid body dynamics for finding protein folding pathway. <br>
<br>
<div class="gmail_quote">On Sat, Dec 31, 2011 at 10:23 AM, <a href="mailto:felmerino@uchile.cl" target="_blank">felmerino@uchile.cl</a> <span dir="ltr"><<a href="mailto:felmerino@uchile.cl" target="_blank">felmerino@uchile.cl</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<p>I small thing to consider with that particular paper is that DE Shaw has a special machine (Anton) to do those calculations, so in principle it is not possible to reproduce them (in a reasonable amount of time) on a regular (super)computer. I think your best shot, if your protein is small enough, is to use accelerated MD mixed with some good old kramer's theory. See for example <cite style="font-family:'Trebuchet MS',Arial,Helvetica,sans-serif;font-size:12px;line-height:16px;text-align:left">J. Chem. Theory Comput.</cite><span style="font-family:'Trebuchet MS',Arial,Helvetica,sans-serif;font-size:12px;line-height:16px;text-align:left">, </span><span style="font-weight:bold;font-family:'Trebuchet MS',Arial,Helvetica,sans-serif;font-size:12px;line-height:16px;text-align:left">2011</span><span style="font-family:'Trebuchet MS',Arial,Helvetica,sans-serif;font-size:12px;line-height:16px;text-align:left">, </span><span style="font-style:italic;font-family:'Trebuchet MS',Arial,Helvetica,sans-serif;font-size:12px;line-height:16px;text-align:left">7</span><span style="font-family:'Trebuchet MS',Arial,Helvetica,sans-serif;font-size:12px;line-height:16px;text-align:left"> (3), pp 575–581.</span></p>
<p>In any case it seems to me like too much of an effort, in the end here you really rely in the accuracy of the forcefield.</p>
<p>Regards</p>
<blockquote><br></blockquote>
<blockquote>----Mensaje original----<br> De: <a href="mailto:jmdamas@itqb.unl.pt" target="_blank">jmdamas@itqb.unl.pt</a><br> Fecha: 30-dic-2011 21:40<br> Para: "Discussion list for GROMACS users"<<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Asunto: Re: [gmx-users] Re: Folding rate
<div>
<div><br> <br> As it was pointed out, the literature is vast on this subject.</div>
</div>
</blockquote>
<div>
<div>
<blockquote>
<div><br></div>
<div>Moreover, calculating folding rates from simulations is not a trivial subject, and it relies on many assumptions (e.g. what is considered "folded", that the sampling obtained is enough). Even for small peptides, "enough sampling" may mean several hundreds of microsseconds, something not accessible to everyone.</div>
<div><br></div>
<div>For a very recent article on the subject, check out:</div>
<div><br></div>
<div>Lindorff-Larsen, K., Piana, S., Dror, R.O., Shaw, D.E. (2011) How Fast-Folding Proteins Fold, <i>Science</i> 334:517-520.</div>
<div><a href="http://dx.doi.org/10.1126/science.1208351" target="_blank">http://dx.doi.org/10.1126/science.1208351</a></div>
<div><br></div>
<div>Regards,</div>
<div>João</div>
<div><br>
<div class="gmail_quote">On Sat, Dec 31, 2011 at 12:19 AM, KS Rotondi <span dir="ltr"><<a href="mailto:ksr@chemistry.umass.edu" target="_blank">ksr@chemistry.umass.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
<div>As Justin pointed out, there is a vast literature on this topic, you need to ask yourself what you seek, and look at many review articles to find some reasonable starting points for you own needs and designs. Beyond that, it's a lot of hard work...</div>
<div>
<div><br>
<div>
<div>On Dec 30, 2011, at 7:04 PM, bharat gupta wrote:</div>
<br>
<blockquote>Thanks for your advice... Could you please refer me some papers regarding this ....<br><br>
<div class="gmail_quote">On Sat, Dec 31, 2011 at 8:17 AM, KS Rotondi <span dir="ltr"><<a href="mailto:ksr@chemistry.umass.edu" target="_blank">ksr@chemistry.umass.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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.<br>
<br> Ken
<div>
<div><br> <br> On Dec 30, 2011, at 6:09 PM, Justin A. Lemkul wrote:<br> <br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br> <br> bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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 ??<br>
</blockquote>
<br> 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.<br>
<br> -Justin<br> <br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">On Sat, Dec 31, 2011 at 8:00 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
bharat gupta wrote:<br> Hi,<br> I want to know whether it's possible to calculate the folding<br> rate of 20 residue peptide folding into a beta-hairpin using<br> gromacs ??<br> Anything is possible ;) But seriously, there is existing literature<br>
on such topics, I suspect you can find methodology that will suit<br> your needs.<br> -Justin<br> -- ==============================__==========<br> Justin A. Lemkul<br> Ph.D. Candidate<br> ICTAS Doctoral Scholar<br>
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