Concept
Protein–protein interaction prediction is a field combining bioinformatics and structural biology in an attempt to identify and catalog physical interactions between pairs or groups of proteins. Understanding protein–protein interactions is important for the investigation of intracellular signaling pathways, modelling of protein complex structures and for gaining insights into various biochemical processes. Experimentally, physical interactions between pairs of proteins can be inferred from a variety of techniques, including yeast two-hybrid systems, protein-fragment complementation assays (PCA), affinity purification/mass spectrometry, protein microarrays, fluorescence resonance energy transfer (FRET), and Microscale Thermophoresis (MST). Efforts to experimentally determine the interactome of numerous species are ongoing. Experimentally determined interactions usually provide the basis for computational methods to predict interactions, e.g. using homologous protein sequences across species. However, there are also methods that predict interactions de novo, without prior knowledge of existing interactions. Proteins that interact are more likely to co-evolve, therefore, it is possible to make inferences about interactions between pairs of proteins based on their phylogenetic distances. It has also been observed in some cases that pairs of interacting proteins have fused orthologues in other organisms. In addition, a number of bound protein complexes have been structurally solved and can be used to identify the residues that mediate the interaction so that similar motifs can be located in other organisms. The phylogenetic profile method is based on the hypothesis that if two or more proteins are concurrently present or absent across several genomes, then they are likely functionally related. Figure A illustrates a hypothetical situation in which proteins A and B are identified as functionally linked due to their identical phylogenetic profiles across 5 different genomes.