Hi,
Does modeller provide a means of generating models that differ only slightly from an input template?
I have been using modeller to generate models of an antibody, and then docking those models to the solved structure of the target antigen protein for that antibody. Multiple models are required, as the docking is very sensitive to the correct conformation of loops at the docking interface. I have some resulting docked conformations that are receiving pretty high ZRANK scores, but upon inspection, it seems that they could all be just a little bit better fit. I was hoping I could feed these docked conformations as templates into modeller, and generate a large number of very similar models, with slightly differing energies.
I'm already comfortable generating input PIR alignments with multiple chains; I'm just interested in hearing what the recommended approach would be for such a refinement process.
Cordially, Jake