Recent improvements in proteomics technology have produced a large volume of protein interaction data. However, understanding protein-protein interactions has not kept pace with the rapidly expanding amount of protein interaction data. In addition to the volume of the data, the difficulties in analyzing protein interaction data come from (1) data is disseminated in many different database, (2) different databases use different HyperText Markup Language (HTML) tags to represent proteins and their interactions, and (3) HTML says nothing about the semantics of a document. This paper presents the development of a new, mobile application for making the task of analyzing protein interaction data easy and customized to individual researchers’ needs. To the best of our knowledge, this is the first mobile application for mining and visualizing bioinformatics data. A HTML parser was developed to extract protein interaction data from remote databases and to construct a local database with the extracted data. A program running on a mobile computer dynamically queries the local protein interaction database and visualizes the query results in three-dimensional space, based on our heuristic layout algorithm. The three-dimensional drawing can be explored further by rotating or by zooming in or out of it. Experimental results demonstrate that this system can be used as useful aids in studying protein-protein interactions in a variety of different environments.