[modeller_usage] Re: Alignment to use when I am modelling a heteromer using a homer as template

[Modeller Caretaker <>]

On 3/18/24 8:13 AM, hmad3--- via modeller_usage wrote:
> I am currently modelling a heteromeric protein using a homomeric
> protein as a template, as follows:
> - heteromer subunits (target): 2 x aaaaaaaa + bbbbbbbbb
> - homomer subunits (template): 3 x cccccccccc
> 
> When aligning the monomer sequences to be used in the .ali file,
> should I align aaaaaaaa and cccccccccc separately, then bbbbbbbbb and
> cccccccccc and use the sequences generated in the FASTA file of each
> alignment in the .ali file -- or should I align all three sequences at
> once and use the sequences in the FASTA file in the .ali file? (In the
> first case, there would be two FASTA files and "cccccccccc" would be
> aligned differently, and both alignments of cccccccccc would be used in
> the .ali file. In the second case, there would be one FASTA file.)

Usually for modeling you would want a single alignment containing all 
the sequences. See the FAQ for an example:
https://salilab.org/modeller/FAQ.html#1

Your alignment would end up looking something like

temp1:  aaaaaaaa/aaaaaaaa/---------*
temp2:  --------/--------/bbbbbbbbb*
target: cccccccc/cccccccc/ccccccccc*

How you produce the alignment (e.g. manually combining two or more 
initial alignments in a text editor) is up to you.

	Ben Webb, Modeller Caretaker
-- 
             https://salilab.org/modeller/
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