Standalone bio-molecular modeling applications with rich functionalities re already abundant. Since they are developed as single-user applications, hose tools cannot be used for remote collaboration, where users want to performbio-molecular structural modeling tasks without being in the same place hysically. Even though other means of collaboration such as emails or chat essaging exist, they are or not real-time (e.g. e-mail) or do not support a hared experience of graphical objects (e.g. Instant Messaging). On the other and, the three-dimensional Internet (3D Internet) is an emerging technology or building world-like environments for real-time collaboration. Therefore, in his paper, we will integrate a standalone bio-molecular application (BALLView) ith an online collaborative virtual world application (OpenMol) to extend he enefits both applications. © 2010 Springer:-Verlag Berlin Heidelberg.