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Failed implantation is the major restraining factor in assisted reproduction and is defined as the ‘black-box of assisted reproduction’. Although work on understanding the complex process of implantation has substantially advanced, it has been limited to studies on mechanism of steroid hormone-mediated signaling during embryo implantation and knocking out single molecules and assessing their impact on embryo implantation. It is important to realize that most proteins exert their function via interaction with other proteins in order to relay downstream signals and/or regulate gene expression via interactions within promoter complexes. Such networks of biomolecular interactions constitute the basis for life as protein interactions are obligatory for cellular functioning. Thus, this review will focus on highlighting protein interactions during the complex process of embryo implantation as they attain a larger significance as pregnancy is fundamental to childbirth and the continuity of life per se.