Hello world,
How can I dock one protein into interface between two proteins? I am new to rosetta software and I am still leraning. I study a protein that bridges two other proteins togeter and I was wondering how can I model that? I would apreciate your input in directing me to the tutorials or documentation.
Thanks. Cheems
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It depends a bit on the protocol you're interested in using, but Rosetta can indeed do protein-protein docking with multimers. The only trick is to make sure you set things up appropriately such that Rosetta knows which chains are mobile and which chains are fixed. (Or equivalently, which chains are on one side of the docking and which are on the other.)
The chains on each side are treated (more-or-less) as a rigid body, so there should be no issues with docking something to the interface between chains. (Again, presuming you have the mobile/fixed chains set properly.)
If you haven't yet, take a look a the Meiler Lab tutorial on protein-protein docking (https://meilerlab.org/rosetta-workshop-2022/), which uses a (multi-chain) antibody as one of the docking partners.
Thnaks for the prompt responce!
While we are on the subject of tutorials. it seems like python scripts in th tutorials use python2.7 but Biopython does not support python2.7. I was reading latest realse notes for Rosetta and it apperas that the comunity is moving towards python3. Does this mean that the scriptis used in tutorails such as cleanPDB.py and reorder_pdb_chains.py were also rewritten in python3?
Thanks. Cheems
It's mixed. The Rosetta community has more or less switched to Python3, but there hasn't necessarily been a push to re-write some of the older scripts. It's been mostly piece-meal, with individuals updating scripts as they need them.
My generally recommendation - if you're working with a script which needs python2.7 - would be to use something like Conda which allows you to create a python2.7-specific environment, and to install Python2.7 versions of various libraries. While the recent versions of Biopython don't support Python2.7, I think there should be older versions availible through pip and/or Conda which would support Python2.7, and pip/conda will either find them automatically, or can be asked to install specifically those versions which support Python 2.7.