The tremendous increase in chemical structure and biological activity data brought about through combinatorial chemistry and high-throughput screening technologies has created the need for sophisticated graphical tools for visualizing and exploring structure-activity data. Visualization plays an important role in exploring and understanding relationships within such multidimensional data sets. Many chemoinformatics software applications apply standard clustering techniques to organize structure-activity data, but they differ significantly in their approaches to visualizing clustered data. Molecular Property eXplorer (MPX) is unique in its presentation of clustered data in the form of heatmaps and tree-maps. MPX employs agglomerative hierarchical clustering to organize data on the basis of the similarity between 2D chemical structures or similarity across a predefined profile of biological assay values. Visualization of hierarchical clusters as tree-maps and heatmaps provides simultaneous representation of cluster members along with their associated assay values. Tree-maps convey both the spatial relationship among cluster members and the value of a single property (activity) associated with each member. Heatmaps provide visualization of the cluster members across an activity profile. Unlike a tree-map, however, a heatmap does not convey the spatial relationship between cluster members. MPX seamlessly integrates tree-maps and heatmaps to represent multidimensional structure-activity data in a visually intuitive manner. In addition, MPX provides tools for clustering data on the basis of chemical structure or activity profile, displaying 2D chemical structures, and querying the data based over a specified activity range, or set of chemical structure criteria (e.g., Tanimoto similarity, substructure match, and "R-group" analysis).