Hi, I have modelled a protein using secondary structure restrained script... The model seems to be perfectly fine .. but one portion of the model is converted into a helix which has to be a loop according to the template .. how can I force that region to be a loop ???
------------ Bharat
Ph.D. Candidate
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On 01/27/2011 06:22 AM, bharat lal wrote: > I have modelled a protein using secondary structure restrained script... > The model seems to be perfectly fine .. but one portion of the model is > converted into a helix which has to be a loop according to the template > .. how can I force that region to be a loop ???
You can't *force* it, but if you unalign the target and template in this region, loop/coil is the most likely secondary structure you'll end up with. See http://salilab.org/archives/modeller_usage/2009/msg00170.html
Ben Webb, Modeller Caretaker
Dear all,
I have a protein consisting of a C-terminal and N-terminal region. While for the C-terminal one I have a good template either Modeller or Blast don't suggest templates for the N-terminal one. I have some suggestion using Modweb (which search performs Modweb?) but not very good. Could ou suggest me a website to search for a template? I looked at the mailing list (very long...) but seems this question has not been posed. Many thanks,
Marco
Dr.Marco Sette, Ph.D.
Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328
--- Gio 27/1/11, Modeller Caretaker modeller-care@salilab.org ha scritto:
> Da: Modeller Caretaker modeller-care@salilab.org > Oggetto: Re: [modeller_usage] Loop modeling > A: "bharat lal" monu46010@yahoo.com > Cc: "modeller" modeller_usage@salilab.org > Data: Giovedì 27 gennaio 2011, 21:44 > On 01/27/2011 06:22 AM, bharat lal > wrote: > > I have modelled a protein using secondary structure > restrained script... > > The model seems to be perfectly fine .. but one > portion of the model is > > converted into a helix which has to be a loop > according to the template > > .. how can I force that region to be a loop ??? > > You can't *force* it, but if you unalign the target and > template in this > region, loop/coil is the most likely secondary structure > you'll end up > with. See > http://salilab.org/archives/modeller_usage/2009/msg00170.html > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org > http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >
On 3/1/11 6:31 AM, Marco Sette wrote: > I have a protein consisting of a C-terminal and N-terminal region. > While for the C-terminal one I have a good template either Modeller > or Blast don't suggest templates for the N-terminal one. I have some > suggestion using Modweb (which search performs Modweb?) but not very > good. Could ou suggest me a website to search for a template? I > looked at the mailing list (very long...) but seems this question has > not been posed. Many thanks,
Since Modeller is a package for comparative modeling, if you don't have a template, you cannot model that region of your model.
I don't know what you mean by "Modeller ... doesn't suggest templates" since Modeller doesn't suggest templates for you. Perhaps you mean you are doing a sequence-sequence search to look for templates (step 1 of the basic tutorial) and you didn't find any? BLAST does essentially the same thing - except that it's using an approximation rather than "real" dynamic programming, so it runs faster - so is also unlikely to find a template if this search doesn't work.
ModWeb supplements this basic sequence-sequence search with more sensitive profile-based searches (it also tries PSI-BLAST, which is a similar method). But there are many other methods available to search for templates - e.g. HMM-based. One thing you could do is look at the best performers for the last CASP contest and see how they detect templates - some of those are available as web servers.
Ben Webb, Modeller Caretaker
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bharat lal -
Marco Sette -
Modeller Caretaker