Hello,
I am trying to model a multichain protein using 2 templates - the .pdb file of an oligomer (with the same number of chains as the target) and the .pdb file of the AlphaFold structure of one of the monomers making up the target protein. (When I model using only the oligomer as target, the model of the target looks quite "off".)
First scenario: * target protein: 5 of the same chain * template protein 1 ("base template"): a homopentamer * template protein 2 ("sub-template" - i.e. the target protein is first modelled based on the first template then modelled based on the 2nd template): the AF predicted structure of one chain of the target protein (the .pdb file has only one chain).
Second scenario: * target protein: a heteropentamer - 2 of one chain + 3 of another chain * template protein 1: as in the previous scenario * template protein 2 (+3): AF predicted structures of the two chains making up the target heteropentamer. There are 2 AF folds, one for each monomer, each one with a single chain.
How would I format the alignment file?
I look forward to your guidance.
Kind regards, Amanda