Embedding Alternative Conformations of Proteins in Protein–Protein Interaction Networks

While many proteins act alone, the majority of them interact with others and form molecular complexes to undertake biological functions at both cellular and systems levels. Two proteins should have complementary shapes to physically connect to each other. As proteins are dynamic and changing their conformations, it is vital to track in which conformation a specific interaction can happen. Here, we present a step-by-step guide to embedding the protein alternative conformations in each protein-protein interaction in a systems level. All external tools/websites used in each step are explained, and some notes and suggestions are provided to clear any ambiguous point.