Table 1. Main hyper-parameters of CCD2PI.

Docked interfaces Distance threshold (in Å)	Predicted interfaces Scoring strategy	Docking energya (E)	Pair potential b (PP)
4.5 5 6	SC-mix SC-monoSeed-mix SC-dockSeed-mix SC-juxt	MAXDo iATTRACT PISA	CIPS None

The default parameter values are highlighted in bold. They were optimized on PPDBv2 (see Methods).

^a MAXDo was chosen for all functional classes but EI and ER, where it was replaced by PISA and iATTRACT respectively.

^b CIPS was used for all functional classes but OR.