competition multimer analysis -- does chain order matter?

[avilella]

Hi,

I want to run what I call a "competition analysis" where I am inputting 3 chains into RosettaFold2, one of them is an antigen, e.g. PD-1, the other is the antigen ligand or cofactor, e.g. PD-L1, and the third is an antibody Fv (heavy and light chains linked with a {GGGGS}x4 linker).

Knowing that there are antibodies that should block the interaction between PD-1 and PD-L1, I noticed that some of the predictions show PD-1 interacting with PD-L1 (chain A and chain B) in the same way as the crystal structure for the PD-1/PD-L1 complex, and then the antibody Fv (chain C) is just binding in the wrong place when considering the experimental data we have about the antibody.

Does the order of the chains matter to RosettaFold2 multimer? If expecting an interacting where chain A + chain B are competing with the interaction of chain A + chain C, does it matter which chains are given first in the input fasta file?

Is there a way to "jolt" the prediction step so that it can leave a local maxima and reattempt the 3 chain prediction iteration in a different configuration? Which parameter would that be? thanks.