I am a beginner in protein modelling/analysis and trying to learn through tutorials and the forums here.
A bit of a background of my present Task: I have a crystal structure of an Ab-Ag complex (AbFab with Ag peptide). I also have experimental data on binding affinities of several Ag peptide variants. I want to use this data to predict binding ability of novel Ag peptide variants with the same Ab.
What I have done so far: Relaxed the Pdb structure to be used with rosetta, added mutations to the peptide using Fixbb, relaxed the structure again, used flexpepdock refine to allow peptide backbone flexibility and finally InterfaceAnalyzer to calculate dG_separated.
My questions: 1) Is this workflow okay? 2) The plan is to build a range of dG_separated values based on experimental data of peptide binders vs Non binders and using those to predict the binding ability of the novel peptide variants. I understand that rosetta doesn't predict binding energies in kcal/mol and uses REU that correlate linearly with binding energy. Our collaborators use RDOCK energy of -6 kcal/mol as an empirically-fixed threshold to distinguish between potential binders and non-binders. Does such a threshold value exist for rosetta?
I'd greatly appreciate any and all suggestions. Thanks!