Although the eukaryotic nucleus is a major actor of the cellular process, its own dynamic and structure are still barely known. However, during the last five years, lot's of studies have shown that, in the nucleus, structure and dynamic are intimately coupled and that it is not possible to understand the former without a complete understanding of the later. Yet, to understand how a complex dynamic leads to such an organized system, we need specific modeling tools. The "Multi-Agent Systems" (MAS) approach will be discussed as an efficient tool to model nuclear dynamic. However, the use of MAS requires a precise methodology to choose the best modeling level (i.e. the description level) depending on the question one wants to address (i.e. depending on the observation level). We will present 3DSPI, a modeling software under development, based on molecular-agents. Our aim is to use 3DSPI to study the emergence of organized multi-protein structures.