Forcing a template to build a missing piece...

[abrol]

Hi,

I would like to use i-tasser in the following manner.

I have a protein-protein (A-B) complex PDB from a cryoEM structure.
B is full-length, but A is missing a piece (ranging between 20-120 residues in length),
that might have its own tertiary structure.

How can I use the PDB of the complex as a template and have i-tasser grow the missing piece in
A in the presence of protein B, without altering the rest of the structure.

Currently, when I input the A-B complex PDB as a template by converting it into a single chain template,
i-tasser grows the missing piece, but also optimizes the known-structure region in the A-B complex that I am happy with.

So, I only want to grow the missing piece without changing the rest of the template.

Is this possible? If yes, how can I implement this?

Thanks,
Ravi

[xiaogenz]

You can try to use our newly developed program DEMO-EM (https://zhanggroup.org/DEMO-EM/) by considering each chain as a virtual domain. Please let us know if you need any help.