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 webbased tool also incorporates both visualization techniques and clustering analysis algorithms to support effective pattern recognition in the molecular self-organization of the clusters.