I searched the archives and could not find how to do what seems to be a simple procedure. I have a sequence that has high homology with a published X-ray structure A. A second state of the protein is defined by the conformation of a conserved loop. A related protein B containing the conserved loop is in the second state, albeit with lower homology. I would like to model the sequence in the second state using the structure A as a template, but using structure B to model the loop only. I believe I need an alignment like this: proteinA aaaaaaaaaaaaaaaa-------------------aaaaaaaaaaaa proteinB ----------------------------bbbbbbbbbbb--------------------- sequence cccccccccccccccccccccccccccccccccccccccccccccc
I realize this is a very simple question. I've been going through the manual and searching the archives and cannot figure out how to do it. Any help will be much appreciated. Thanks. EGY
Have you tried it and didn't work? This is how the alignment should look like. Just remember to superimpose the two templates (A, B) so that the loop ends look "joined".
On 7 May 2012 16:14, EGY mp.2egy@gmail.com wrote:
> I searched the archives and could not find how to do what seems to be a > simple procedure. I have a sequence that has high homology with a published > X-ray structure A. A second state of the protein is defined by the > conformation of a conserved loop. A related protein B containing the > conserved loop is in the second state, albeit with lower homology. I would > like to model the sequence in the second state using the structure A as a > template, but using structure B to model the loop only. I believe I need an > alignment like this: > proteinA aaaaaaaaaaaaaaaa-------------------aaaaaaaaaaaa > proteinB ----------------------------bbbbbbbbbbb--------------------- > sequence cccccccccccccccccccccccccccccccccccccccccccccc > > I realize this is a very simple question. I've been going through the > manual and searching the archives and cannot figure out how to do it. Any > help will be much appreciated. > Thanks. > EGY > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >
Also allow for some overlap to ensure loop closure. I.e.
proteinA aaaaaaaaaaaaaaaa---------aaaaaaaaaaaa proteinB -----------------------bbbbbbbbbbb---------------- sequence cccccccccccccccccccccccccccccccccc
On 7 May 2012 16:21, Thomas Evangelidis tevang3@gmail.com wrote:
> Have you tried it and didn't work? > This is how the alignment should look like. Just remember to superimpose > the two templates (A, B) so that the loop ends look "joined". > > > > On 7 May 2012 16:14, EGY mp.2egy@gmail.com wrote: > >> I searched the archives and could not find how to do what seems to be a >> simple procedure. I have a sequence that has high homology with a published >> X-ray structure A. A second state of the protein is defined by the >> conformation of a conserved loop. A related protein B containing the >> conserved loop is in the second state, albeit with lower homology. I would >> like to model the sequence in the second state using the structure A as a >> template, but using structure B to model the loop only. I believe I need an >> alignment like this: >> proteinA aaaaaaaaaaaaaaaa-------------------aaaaaaaaaaaa >> proteinB ----------------------------bbbbbbbbbbb--------------------- >> sequence cccccccccccccccccccccccccccccccccccccccccccccc >> >> I realize this is a very simple question. I've been going through the >> manual and searching the archives and cannot figure out how to do it. Any >> help will be much appreciated. >> Thanks. >> EGY >> _______________________________________________ >> modeller_usage mailing list >> modeller_usage@salilab.org >> https://salilab.org/mailman/listinfo/modeller_usage >> > > > > -- > > ====================================================================== > > Thomas Evangelidis > > PhD student > > Biomedical Research Foundation, Academy of Athens > > 4 Soranou Ephessiou , 115 27 Athens, Greece > > email: tevang@bioacademy.gr > > tevang3@gmail.com > > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > >
Sorry, my question is much more elementary. I see an example from the tutorial (Advanced Modeling, Modeling ligands in the binding site) on an alignment similar to what I want. However, I don't see the associated script to give this alignment, only the resulting pap file. In this example, only the binding pocket of the 1emd structure was included in the alignment. I would also need to know how not to include a region in one of the other sequences. Thanks.
On May 7, 2012, at 9:43 AM, Thomas Evangelidis wrote:
> Also allow for some overlap to ensure loop closure. I.e. > > proteinA aaaaaaaaaaaaaaaa---------aaaaaaaaaaaa > proteinB -----------------------bbbbbbbbbbb---------------- > sequence cccccccccccccccccccccccccccccccccc > > > On 7 May 2012 16:21, Thomas Evangelidis tevang3@gmail.com wrote: > Have you tried it and didn't work? > This is how the alignment should look like. Just remember to superimpose the two templates (A, B) so that the loop ends look "joined". > > > > On 7 May 2012 16:14, EGY mp.2egy@gmail.com wrote: > I searched the archives and could not find how to do what seems to be a simple procedure. I have a sequence that has high homology with a published X-ray structure A. A second state of the protein is defined by the conformation of a conserved loop. A related protein B containing the conserved loop is in the second state, albeit with lower homology. I would like to model the sequence in the second state using the structure A as a template, but using structure B to model the loop only. I believe I need an alignment like this: > proteinA aaaaaaaaaaaaaaaa-------------------aaaaaaaaaaaa > proteinB ----------------------------bbbbbbbbbbb--------------------- > sequence cccccccccccccccccccccccccccccccccccccccccccccc > > I realize this is a very simple question. I've been going through the manual and searching the archives and cannot figure out how to do it. Any help will be much appreciated. > Thanks. > EGY > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > > > > -- > ====================================================================== > Thomas Evangelidis > PhD student > Biomedical Research Foundation, Academy of Athens > 4 Soranou Ephessiou , 115 27 Athens, Greece > > email: tevang@bioacademy.gr > tevang3@gmail.com > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > > > > -- > ====================================================================== > Thomas Evangelidis > PhD student > Biomedical Research Foundation, Academy of Athens > 4 Soranou Ephessiou , 115 27 Athens, Greece > > email: tevang@bioacademy.gr > tevang3@gmail.com > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage
On 5/7/12 7:35 AM, EGY wrote: > Sorry, my question is much more elementary.
Your original question was addressed just last week on the mailing list: http://salilab.org/archives/modeller_usage/2012/msg00152.html
> I see an example from the tutorial (Advanced Modeling, Modeling > ligands in the binding site) on an alignment similar to what I want. > However, I don't see the associated script to give this alignment
You make the alignment yourself, e.g. in a text editor. There is no script to generate it for you automatically.
> In this example, only the binding pocket of the 1emd structure was > included in the alignment. I would also need to know how not to > include a region in one of the other sequences.
Either edit the PDB file to remove the region you don't want to include, or see http://salilab.org/modeller/9.10/FAQ.html#2
Ben Webb, Modeller Caretaker
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EGY -
Modeller Caretaker -
Thomas Evangelidis