Comparative modeling
The outline of multimeric comparative modeling pipeline is provided in
Supplementary Figure S1. Starting with target sequences, we first
searched for potential templates using PPI3D18 and
HHpred19, 20 web servers. If this step failed to
identify reliable templates, we additionally employed structure-based
searches. In this case, selected monomeric CASP server models
corresponding to the subunits of a target protein complex were used as
queries for PDB searches using the DALI server21. The
aim was to identify multimeric PDB assemblies that could potentially
serve as multimeric templates. Once templates were identified using
either sequence- or structure-based searches, structural models for the
whole protein complex were generated by MODELLER22 and
its plugin AltMod23 using the multi-chain modeling
function.