Protein-protein interaction networks often consist of thousands of nodes or more, which severely limit the usefulness of many graph drawing tools because they become too slow for interactive anal- ysis of the networks and because they produce cluttered drawings with many edge crossings. We present a new, extremely fast layout algorithm and its implementation called InterViewer3 for visualizing large-scale protein interaction networks. InterViewer3 (1) first finds a layout of connected components of an entire network, (2) finds a global layout of nodes with respect to pivot nodes within a connected component, and (3) refines the local layout of each connected component by first relocating midnodes with respect to their cutvertices and direct neighbors of the cutvertices and then by relocating all nodes with respect to their neighbors within distance 2. Advantages of InterViewer3 over classical graph drawing methods include: (1) it is an order of magnitude faster, (2) it can directly visualize data from protein interaction databases, and (3) it provides several operations for effectively exploring large-scale protein interaction networks.
