All living organisms are complex systems, of which all functions rely on complicated and extensive interactions of biological molecules. A number of articles covering various aspects of molecular interactions have been published in previous issues of JMCB, including two special issues on complex diseases-related bio-networks (Chen and Wu, 2012, 2015). This collection of recent research findings involving protein interaction, modification, and regulation will add new information to understanding the biological functions based on protein interplays.