optimisation of a protein-protein interface

[Anonymous]

Dear Rosetta users,

I have a symmetrical homo-dimeric structure for which I would like to select a single point mutation that will increase the affinity between the monomers.
I thought about design&relax protocol, in which one position is designed while the remaining ones are only allowed to repack. Such a protocol would be used to scan all the interface positions.

My questions is how to set up this in Rosetta Scripts? Perhaps there are easier/better ways to do this?

Thanks for help!
Staszek

[Anonymous]

If you’re looking for single point mutations, the pmut scan protocol  may be what you want to use. This isn’t through RosettaScripts, though, so the control of the relaxation protocol might be less flexible than you want.

Another option is to use the GreedyOptMutationMover. This is originally intended as a “polishing” mover for designs (see https://doi.org/10.1002/prot.24463), but it contains a mutation scan protocol that you can obtain the intermediate table from. I’ve used this in the past to do mutational scanning.

The final approach is to just set up the 20xN different resfiles, each with the different point mutation, and run those through a standard design/optimization run.

[Anonymous]

If you’re looking for single point mutations, the pmut scan protocol  may be what you want to use. This isn’t through RosettaScripts, though, so the control of the relaxation protocol might be less flexible than you want.

Another option is to use the GreedyOptMutationMover. This is originally intended as a “polishing” mover for designs (see https://doi.org/10.1002/prot.24463), but it contains a mutation scan protocol that you can obtain the intermediate table from. I’ve used this in the past to do mutational scanning.

The final approach is to just set up the 20xN different resfiles, each with the different point mutation, and run those through a standard design/optimization run.

[Anonymous]

If you’re looking for single point mutations, the pmut scan protocol  may be what you want to use. This isn’t through RosettaScripts, though, so the control of the relaxation protocol might be less flexible than you want.

Another option is to use the GreedyOptMutationMover. This is originally intended as a “polishing” mover for designs (see https://doi.org/10.1002/prot.24463), but it contains a mutation scan protocol that you can obtain the intermediate table from. I’ve used this in the past to do mutational scanning.

The final approach is to just set up the 20xN different resfiles, each with the different point mutation, and run those through a standard design/optimization run.

[Author]

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