I recently read a paper from Xencor describing their excellent work on mutation design of antibody Fc regions to increase the binding affinity to Fc-gamma receptor III-A and consequently enhance the Fc effector function. In the original paper's supporting text of method (http://www.pnas.org/content/suppl/2006/03/02/0508123103.DC1/08123SuppText.pdf), it mentioned a computation method called PDA which was invented by Dr. Mayo in 1996. Since Mayo was cofounder of MSI and later Accelrys, so I guess this method may become part of Accelrys discovery studio (I am not sure).
since Rosetta is versatile modeling suite, I am trying to use Rosetta to repeat the whole design process of that paper. I think RosettaDesign could be the starting point, however I also think a customized RosettaXML script could be fit for the purpose of iterative design cycles.
I am wondering if someone is also interested in using Rosetta to do this design. I need some enlightments from your expertise. Thanks.
There is currently ongoing work on antibody design, but mainly in the Fv, primarily in the CDRs (in preparation). I could certainly help with constructing an XML or PyRosetta script to do the type of design that you are after - but I don't think there is any extremely specific design algorithm implemented to handle this type of thing.