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Information on protein-protein interactions (PPIs) not only advances ourunderstanding of molecular biology but also provides important clues for targetselection in drug discovery and the design of PPI inhibitors. One of thetechniques used for computational prediction of PPIs is protein-protein dockingcalculations, and a variety of software has been developed. However, a friendlyinterface for users who are not sufficiently familiar with the command lineinterface has not been developed so far. In this study, we have developed agraphical user interface, MEGADOCK-GUI, which enables users to easily predictPPIs and protein complex structures. In addition to the original 3-D molecularviewer and input file preparation functions, MEGADOCK-GUI is software that canautomatically perform complete cross-docking of $M$ vs. $N$ proteins. WithMEGADOCK-GUI, various applications related to the prediction of PPIs, such asensemble docking that handles multiple conformations of proteins and screeningof binding partner proteins that bind to specific proteins, can now be easilyperformed.

MEGADOCK-GUI: a GUI-based complete cross-docking tool for exploring protein-protein interactions