Nucleation phenomena play a pivotal role in many atmospheric and technological processes. However, understanding atmospheric nucleation processes has been difficult due to the lack of effective data exploration tools. In this paper, we present a web-based tool that allows remote users to mine the wealth of particle-based nucleation simulation data through web-based visualization and analysis. The simple yet effective web-based user interface is designed to support collaborative research in the area of atmospheric nucleation. The web-based tool also incorporates both visualization techniques and clustering analysis algorithms to support effective pattern recognition in the molecular self-organization of the clusters.