Rosetta has some applications that can be used to setup a protocol to compute the ddG of binding upon mutation (relax, fixbb or ddg_monomer to create wt structure and mutated structure, InterfaceAnalyzer to compute binding energies, etc.) Are there references available where Rosetta is used this way? Until now I have found papers where the authors either fit their own energy function to experimental data (instead of using Rosetta's energy function), or they use other applications (molecular dynamics, for example) to relax their structures, or something else. I am interested in papers where the authors use Rosetta proper to compute the ddG of binding upon mutations (single or multiple).
Two I can think of at the moment might be interesting:
"Structure-based Protocol for Identifying Mutations that Enhance Protein-Protein Binding Affinities" http://dx.doi.org/10.1016%2Fj.jmb.2007.05.096 This is a little on the old side, though.
"Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing." http://www.ncbi.nlm.nih.gov/pubmed/22634563 - This goes a bit beyond point mutations, though.