Hi there:
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
Jessica
Category:
Post Situation:
Dear Jessica,
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
Best,
Jeliazko