Constructing structural networks of signaling pathways on the proteome scale

► Structural networks are more informative than classical 'nodes-and-edges' networks. ► Structural networks differentiate between competitive and simultaneous binding. ► Structural networks can help drug design and may forecast some side effects. ► We outline how to construct structural networks on a large scale using PRISM. ► We construct the structural network of ERK proteins in the MAPK signaling pathway.