Joint submission from Bindcraft 2 team. Bindcraft 2 expands on the existing capabilities of Bindcraft 1. Specifically we have introduced novel binder targeting capabilities as well as intrinsically disordered region binding code.

While ipTM correlates with binding affinity, it remains prone to false positives, often overlooking legitimate binders with lower scores. To address these limitations, we introduce novel binding site compatibility ranking framework. This method is computationally efficient and has superior correlation with experimental affinity.

In addition we implemented new approach to design binders against disordered regions. This method overcomes previous preferential binding of Bindcraft 1 to ordered protein regions.

Finally we also used advanced filtering algorithms to reduce false positive binders.

The submitted binders use a mix of these techniques and are ordered according to our internal ranking system.