multi state protein design

[Anonymous]

Hello,

I have an enzyme and I want to optimize its sequence to increase its binding to one protein and decrease its binding to another protein at the same time. I recently attended Rosetta workshop and learn about multi state protein design which can be used to increase affinity of an antibody to its ensemble of antigen, but I am not sure whethe it is applicable to my case. I would appreciate any suggestions.

[Anonymous]

Rosetta has at least two multistate design tools.

mpi_msd (https://www.rosettacommons.org/docs/latest/application_documentation/design/mpi-msd) (https://www.rosettacommons.org/demos/latest/protocol_capture/multistate_apl/README) will definitely work for this purpose.  You can set up explicitly negative states for the decreased binding desired.

RECON probably will as well.

[Anonymous]

RECON currently does not handle negative design. It will only work with systems where you’re attempting to improve the energy of all states.

[Author]

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