Transmembrane homodimers/mp_ddG_pipeline

[aozalevsky]

Thanks for the awesome pipeline. I've already got nice results for a monomeric protein, now I'm trying to run a homodimer but not sure if I'm doing it right.

I saw #46 but it doesn't have any specifics about additional keys/modifications to the input. I'm specifically concerned about the format of the span file. Judging by the call in the sbatch script, the span file for only one chain is passed.

Can you give me advice on how to properly run a stability calculation for a transmembrane homodimer with identical mutations in both chains?

Thanks in advance!

[aozalevsky]

just a small bump in case a previous notification got lost.

[j0kaso]

Hi! thanks for the poke and sorry for the late reply - I actually did miss the first comment.

In the automatic tests are a few examples for the different possibilities to run the pipeline - regarding homodimers, here would be the code/input (which you also finde under "test"): https://github.com/KULL-Centre/PRISM/blob/main/software/rosetta_ddG_pipeline/test/test_mp_pipeline.py#L613

For preparation of the pdb file and a suitable mutation input file (needed, otherwise it will not perform the mutations in all chains at the same time), you need some pre-requirements:

• first run pdb_to_prism(https://github.com/KULL-Centre/PRISM/blob/main/software/scripts/pdb_to_prism.py) on the monomer (or just one chain) to get the prism-file info
• use this prism-file and your multi-mere as input for homo_dimer (https://github.com/KULL-Centre/PRISM/blob/main/software/scripts/homo_dimer.py) or homo_oligomers (https://github.com/KULL-Centre/PRISM/blob/main/software/scripts/homo_oligomer.py) to generate the “final” mutation input for the pipeline. Along this, also a freshly renumbered and re-chained (all chains to A) pdb will be generated that you should use as your input for the pipeline
• run the pipeline with chainid=A, the mutations=pipeline_mutfile.txt and mutate_mode=mut_file

Hope that helps! Let me know if anything doesn't work or is unclear :)

[aozalevsky]

awesome, thank you so much for such a detailed response!