[gmx-users] Re: Folding rate
felmerino at uchile.cl
felmerino at uchile.cl
Sat Dec 31 02:23:02 CET 2011
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 J. Chem. Theory Comput., 2011, 7 (3), pp 575–581.
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.
Regards
----Mensaje original---- De: jmdamas at itqb.unl.pt Fecha: 30-dic-2011 21:40 Para: "Discussion list for GROMACS users"<gmx-users at gromacs.org> Asunto: Re: [gmx-users] Re: Folding rate As it was pointed out, the literature is vast on this subject.
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.
For a very recent article on the subject, check out:
Lindorff-Larsen, K., Piana, S., Dror, R.O., Shaw, D.E. (2011) How Fast-Folding Proteins Fold, Science 334:517-520.
http://dx.doi.org/10.1126/science.1208351
Regards,
João
On Sat, Dec 31, 2011 at 12:19 AM, KS Rotondi <ksr at chemistry.umass.edu> wrote:
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...
On Dec 30, 2011, at 7:04 PM, bharat gupta wrote:
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://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> ==============================__========== -- gmx-users mailing list gmx-users at gromacs.org <mailto:gmx-users at gromacs.org> http://lists.gromacs.org/__mailman/listinfo/gmx-users <http://lists.gromacs.org/mailman/listinfo/gmx-users> Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search <http://www.gromacs.org/Support/Mailing_Lists/Search> before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org <mailto:gmx-users-request at gromacs.org>. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists <http://www.gromacs.org/Support/Mailing_Lists> -- 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 <mailto:monu46010 at yahoo.com>
-- ======================================== 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 ======================================== -- gmx-users mailing list gmx-users at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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-- BharatPh.D. CandidateRoom No. : 7202A, 2nd FloorBiomolecular Engineering LaboratoryDivision of Chemical Engineering and Polymer SciencePusan National University Busan -609735South KoreaLab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680E-mail : monu46010 at yahoo.com
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-- João M. Damas PhD StudentProtein Modelling GroupITQB-UNL, Oeiras, PortugalTel:+351-214469613
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