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Recent improvements in high-throughput proteomics technology have produced a large amount of protein interaction data. Due to the volume of data, a graphical representation of protein interactions has proven to be much easier to understand than a long list of interacting proteins. For the past years we have studied the interactions between virus proteins and host cell proteins, but most methods that are typically used for visualizing protein interactions are not appropriate for the interactions between proteins of different types. These methods are intended for the interactions between proteins of a same type, and do not distinguish the interactions between proteins of a same type from those of different types. Visualization of the interactions between different types of proteins (such as virus proteins and host cell proteins) requires a new graph layout algorithm. This paper discusses a new layout algorithm for visualizing the interactions between heterogeneous proteins, and its application to the interactions between virus proteins and human proteins.