Department of Chemical and Biological EngineeringDepartment of Computer Engineering2024-11-0920120959-440X10.1016/j.sbi.2012.04.0042-s2.0-84862625522http://dx.doi.org/10.1016/j.sbi.2012.04.004https://hdl.handle.net/20.500.14288/11254Proteins function through their interactions, and the availability of protein interaction networks could help in understanding cellular processes. However, the known structural data are limited and the classical network node-and-edge representation, where proteins are nodes and interactions are edges, shows only which proteins interact; not how they interact. Structural networks provide this information. Protein-protein interface structures can also indicate which binding partners can interact simultaneously and which are competitive, and can help forecasting potentially harmful drug side effects. Here, we use a powerful protein-protein interactions prediction tool which is able to carry out accurate predictions on the proteome scale to construct the structural network of the extracellular signal-regulated kinases (ERK) in the mitogen-activated protein kinase (MAPK) signaling pathway. This knowledge-based method, PRISM, is motif-based, and is combined with flexible refinement and energy scoring. PRISM predicts protein interactions based on structural and evolutionary similarity to known protein interfaces.BiochemistryMolecular biologyCell biologyJournal Article1879-033X306347800016Q14583