I am working on antibody engineering and have couple of questions about SnugDock function in ROSIE.
1. I used SnugDock to perform local docking for an antibody-antigen complex and I performed both “fast” and “thorough” modes. But for the result, I found there was a docking funnel in “fast” mode and no docking funnel in “thorough”. The SnugDock document said the result of “thorough” and “fast” mode may slightly different. So, why the result of two modes I performed was huge different? And is this mean the docking fail? Since the “thorough” mode do not have docking funnel.
2. Now, I want to use SnugDock to dock an antigen to an antibody and find the binding pose of the complex. I have already used global docking to generate couple of possible binding poses of complex and input to local docking. So, my question is how can I judge which binding pose may be the near-native structure through the docking result. I noticed there was a question about “how to judge docking success without native structure” in Rosetta forums. But I not sure my understanding about the answer is right. For my situation, is this mean I make each possible binding pose from global docking as “native structure”, then perform local docking for them and see whether there is docking funnel in each binding pose result. If one of binding pose result has docking funnel and the other do not, is this mean the binding pose which has docking funnel more likely close to real native structure?