Information on protein-protein interactions (PPIs) not only advances our understanding of molecular biology but also provides important clues for target selection in drug discovery and the design of PPI inhibitors. One of the techniques used for computational prediction of PPIs is protein-protein docking calculations, and a variety of software has been developed. However, a friendly interface for users who are not sufficiently familiar with the command line interface has not been developed so far. In this study, we have developed a graphical user interface, MEGADOCK-GUI, which enables users to easily predict PPIs and protein complex structures. In addition to the original 3-D molecular viewer and input file preparation functions, MEGADOCK-GUI is software that can automatically perform complete cross-docking of $M$ vs. $N$ proteins. With MEGADOCK-GUI, various applications related to the prediction of PPIs, such as ensemble docking that handles multiple conformations of proteins and screening of binding partner proteins that bind to specific proteins, can now be easily performed.