Forcing a template to build a missing piece...

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abrol
Posts: 1
Joined: Mon Dec 13, 2021 8:07 am

Forcing a template to build a missing piece...

Post by 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
Posts: 157
Joined: Sun Apr 25, 2021 12:02 am

Re: Forcing a template to build a missing piece...

Post by 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.
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