Docking

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:

Hi:

Is there a rosetta or pyrosetta script  (or general protocol) you would recommend for a pdb that already has a small molecule ligand docked in a low resolution docking model?

I used Zhang lab's BP Slim server to get this lo res docking, and now what I need to do is refine that model to high res, atomic scale.

thank you all so much, I am learning rapidly from this most generous and helpful community.  - Amy

I am contacting you because I am getting an error in results with Rosetta. Successfully finished protein-protein docking. I can see in the output that following lines complaining about missing atoms. I have prepared protein in ICM, Molsoft. I checked the input file those I have given as input.pdb, there were no missing any CB atoms in all amino acid. Docking finished successfully and generated score value. Do you think this missing atom will make any impact in score value? Let me know how can solve this problem. 

Dear Ligand binding Team,

I am writting this letter of appreciation to thank the team of Rosie Ligand Docking for making available such a powerful docking tool for researchers. We recently used the tool and got wonderful results using a difficult protein (oxidosqualene cyclase). We also want to thank you for making rarely available docking tool based on Induced-Fit freely available to academic users.

We hope that you continue providing the Rosie tools and keep updating the excellent Ligand Docking tool.