Dear Marco, Your question is very nice. But to make a good prediction, better check out structural similarity in templates based on the both N & C terminal. I guess you are modeling a big sequence, which may have multiple domains. So you should consider many things. If you upload other details of the sequence along with its length, it will be better to suggest the best way to screen significant template folds.
Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA
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,
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: email@example.com e-mail: firstname.lastname@example.org Tel.: +39-0672594424 Fax: +39-0672594328
--- Gio 27/1/11, Modeller Caretaker email@example.com ha scritto:
> Da: Modeller Caretaker firstname.lastname@example.org > Oggetto: Re: [modeller_usage] Loop modeling > A: "bharat lal" email@example.com > Cc: "modeller" firstname.lastname@example.org > Data: Gioved? 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 > -- > email@example.com? > ? ? ? ? ???http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > _______________________________________________ > modeller_usage mailing list > firstname.lastname@example.org > https://salilab.org/mailman/listinfo/modeller_usage >
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End of modeller_usage Digest, Vol 10, Issue 41 **********************************************