Hi everyone,
I am working on a multiprotein system. 2 of the subunits have multiple
missing regions. Since the structural template we use is unpublished we
want to refrain from using any webservers. I used the sequence info alone
to model the 2 subunits using alphafold3, then aligned it to the template
and pasted the sequence of the missing region alone. This however resulted
in some clashes and some cispeptide (non proline). I have 2 queries:
1. Do we have any tool in AMBER which might help us fix the cispeptide
problem?
2. How to predict the protonation states? I am aware of the H++ server. But
I wonder if there is someway without uploading our unpublished structure
into the server.
3. Is there any discrepancy in the method I am using to fill the missing
residues?
This is the first time I am working with a multiprotein system with really
large number of missing region which likely are not just loops.
Thank you for any insights you can provide.
-Jenny
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Received on Thu May 22 2025 - 10:00:02 PDT
