Free docking
When no templates could be found for protein complexes, free docking of
top 5 selected monomeric CASP server models was done by
Hex26 for hetero-complexes and Sam27for homomultimers (Supplementary Figure S2). The resulting models were
ranked using global and interaction interface VoroMQA scores as
described below. Next, top 100-500 models were relaxed by a very short
molecular dynamics simulation using OpenMM software28,
Amber99SB force field and GBSA-OBC solvation model29,
30. The relaxed models were subsequently re-ranked using the same
scoring procedure and clustered according to the interface
CAD-score31, 32 values aiming to select a diverse set
of models.