Hello,
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.)
I look forward to your response.
Kind regards, Amanda