Antigen antibody docking

How do I select the best pose when the L-RMSD calculation is not posibilbe as refrence structure is not available ?

In principle based on the HADDOCK score.

Check also our antibody-antigen tutorial at Education & Tutorials of the Bonvin Lab – Bonvin Lab

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what is the best/suitable HADDOCK score?

How can I select the best model from top 4 models within a cluster? What are their individual scores within a cluster?

The HADDOCK score itself! :slight_smile:

The first model of a cluster is always the best one in score.

But you might look at all of them to get an idea of the variability within one cluster