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.
On Sat, Dec 31, 2011 at 10:23 AM, felmer...@uchile.cl <felmer...@uchile.cl>wrote: > 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: jmda...@itqb.unl.pt > Fecha: 30-dic-2011 21:40 > Para: "Discussion list for GROMACS users"<gmx-users@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 <k...@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 <k...@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 <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 >>>>> 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@gromacs.org >>>>> <mailto:gmx-users@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-requ...@gromacs.org >>>>> <mailto:gmx-users-requ...@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 : monu46...@yahoo.com <mailto:monu46...@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@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-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>> >>> -- >>> gmx-users mailing list gmx-users@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 thewww >>> interface or send it to gmx-users-requ...@gromacs.org. >>> >>> Can't post? Read 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 : monu46...@yahoo.com >> >> -- >> gmx-users mailing list gmx-users@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-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> -- >> gmx-users mailing list gmx-users@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-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > João M. Damas > PhD Student > Protein Modelling Group > ITQB-UNL, Oeiras, Portugal > Tel:+351-214469613 > > > > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read 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 : monu46...@yahoo.com
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