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In this chapter, we describe a practical protocol of the tag-based pull-down assay and discuss solutions to some common problems associated with this assay.The yeast two-hybrid (Y2H) system is an effective means of detecting protein-protein interactions through the activation of reporter gene expression. This system has also displayed several useful applications, including rapidly revealing unexpected interactors of known proteins, detecting regions that take part in protein-protein interactions, and characterizing the orchestration of