I use snugDocking to Dock different antibody- antigens. I wonder how could I determine good binding vs bad binding from the result web page.
I am currently decide by look at 1. interface score 2, similarity of top 10 models. If the interface score is low and top 10 models have a couples model in similar position, I assume it is good binding, otherwise It isn't
give an example:
https://rosie.graylab.jhu.edu/snug_dock/viewjob/70005 I assume the binding is good
https://rosie.graylab.jhu.edu/snug_dock/viewjob/70015 I assume the binding is not very good.
Is this method correct?
Thanks and regards
In general, you are correct. Just so you are aware, score itself is not sufficient to identify good binding, especially when comparing multiple complex. There is a nice paper about this here: https://www.nature.com/articles/s41598-017-08414-y