completing incomplete templates
Hello Modeller
I have a newbie question. I have a template structure that is incomplete. There are a couple of segment loops missing. Is it possible to use Modeller to build up the loops if I give it a complete sequence (fasta) and use the template (with missing loops)? The reason I ask is because it was suggested from another web site that Modeller could do this, but I am not convinced that it can.
If not, could someone suggest a software package that could do this?
Thanks for your response
Steve
Steve Seibold
Research Asst. Professor
seibold@chemistry.msu.edu
19B Chemistry Building
Michigan State University
East Lansing, MI 48824
Office 517-355-9715 ext 264
Hello Steve,
A reply from a newbie as well :)
If I understood your question correctly you have more or less this situation:
TEMPLATE AAAAAAAAAA----------AAAAAAAAA SEQUENCE AAAAAAAAAABBBBBBBBBBAAAAAAAAA
If you use the FASTA sequence of your template with its own structure, it will build a complete structure with those sections modelled as loops. You just need to provide MODELLER with the template structure, it's sequence (with gaps in the missing regions), and the sequence of the full thing.
Best Regards,
João [ .. ] Rodrigues
(Blog) http://doeidoei.wordpress.com (MSN) always_asleep_@hotmail.com (Skype) rodrigues.jglm
João Rodrigues wrote: > A reply from a newbie as well :) > > If I understood your question correctly you have more or less this > situation: > > TEMPLATE AAAAAAAAAA----------AAAAAAAAA > SEQUENCE AAAAAAAAAABBBBBBBBBBAAAAAAAAA > > If you use the FASTA sequence of your template with its own structure, > it will build a complete structure with those sections modelled as > loops. You just need to provide MODELLER with the template structure, > it's sequence (with gaps in the missing regions), and the sequence of > the full thing.
Exactly right. There is a worked example in the wiki as well: http://salilab.org/modeller/wiki/Missing%20residues
Ben Webb, Modeller Caretaker
participants (3)
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João Rodrigues -
Modeller Caretaker -
Steve Seibold