Dear, thanks for you help. should i use the the entire second template(loop is disordered) sequence or only part of the disordered sequence to aglian? >Message: 1 >Date: Fri, 03 May 2013 10:31:56 -0700 >From: Modeller Caretaker modeller-care@salilab.org >To: aixintiankong aixintiankong@126.com >Cc: modeller_usage@salilab.org >Subject: Re: [modeller_usage] how to build the loop of protein model > using modeller >Message-ID: 5183F48C.7010601@salilab.org >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >On 4/29/13 8:25 PM, aixintiankong wrote: >> i don't know how to build a model that the protein, NAD+ and ligand >> coexsit and the loop of protein is disordered. > >One way to do this would be to align your model sequence with the first >template (loop is helix) for the entire sequence except the loop, and >the second template (loop is disordered) for the loop: >http://salilab.org/modeller/9.11/FAQ.html#1 > >Another way would be to just use the first template, and just unalign >the loop so Modeller builds it without template information: >http://salilab.org/modeller/9.11/FAQ.html#2 > > Ben Webb, Modeller Caretaker >-- >modeller-care@salilab.org http://www.salilab.org/modeller/ >Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
On 5/8/13 12:37 AM, aixintiankong wrote: > thanks for you help. should i use the the entire second template(loop is > disordered) sequence or only part of the disordered sequence to aglian?
You would definitely need to exclude the ligand and any part of the sequence that interacts with the loop (otherwise Modeller will have a hard time positioning the ligand, since it will get conflicting information). But you can include the rest of the protein if you want - since you said the sequences are very similar I doubt it would make much difference either way.
Ben Webb, Modeller Caretaker
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aixintiankong -
Modeller Caretaker