I recently start to use Pymol for protein protein interaction study.
My protein candidates have co-expression profile (predicted by Genemania and String) and same localization; some of them contains shared protein domain. Then I created 3D structure pdb file of those proteins and loaded them into Pymol, some of them can assemble together a complex and some fall apart.
here comes my question, can I conclude those which can assemble a complex are putative interacting partners. or I need some more evidence.