Dear all
I would like implement the most recent/accurate all-atom Rosetta protocols. In other words, 2 rounds, in the first of which quick backbone models are generated and clustered (the aa protocol). In round 2, members of the largest clusters are all-atom modelled (the cc relax protocol), reclustered and the lowest energy model of the largest cluster taken as the final model. I have a few queries
- can the modelling of homologs of the target (Bradley et al 2005) be done automatically?
- is there a consensus view on whether single or multiple models should be generated from each starting point in round 2? (this was the subject of a previous thread but no clear opinion seemed to emerge)
- can Rosetta cluster the all-atom models at the end of round 2? the rosetta_scripts/abinitio/bin/cluster.pl script, as far as I can tell, works with a silentfile which would be the result of a single run, and would only contain backbone in any case. If Rosetta can't, what tools would people recommend?
Many thanks in advance
Dan
Please check the following answers from Dr Bradley.
> Dear all
>
> I would like implement the most recent/accurate all-atom Rosetta protocols. In other words, 2 rounds, in the first of which quick backbone models are generated and clustered (the aa protocol). In round 2, members of the largest clusters are all-atom modelled (the cc relax protocol), reclustered and the lowest energy model of the largest cluster taken as the final model. I have a few queries
>
> - can the modelling of homologs of the target (Bradley et al 2005) be done automatically?
Not that I'm aware of. I did this using a collection of python scripts which have fallen into disuse.
> - is there a consensus view on whether single or multiple models should be generated from each starting point in round 2? (this was the subject of a previous thread but no clear opinion seemed to emerge)
My opinion would be that multiple models, say 3-5 should be generated due to the stochastic nature of the refinement protocol.
> - can Rosetta cluster the all-atom models at the end of round 2? the rosetta_scripts/abinitio/bin/cluster.pl script, as far as I can tell, works with a silentfile which would be the result of a single run, and would only contain backbone in any case. If Rosetta can't, what tools would people recommend?
I'm not aware of all-atom clustering functionality in Rosetta.
> Many thanks in advance
>
> Dan
Just to say thanks for these thoughts. Much appreciated. It's a real luxury to get first-hand opinions from the people behind Rosetta.
Dan