This work aims to demonstrate how the requirement of modeling complex systems as the biological ones and the advances in multi-agent systems are combined to give a simple, scalable, robust and reliable simulation system. The mobility feature of the BESA agent framework and an interaction biological model are the basis for the construction of a molecular simulation application. The main bioinformatics application's requirements, such as the big number of interacting entities, the high calculations volume, its parallel and distributed processing nature and the need of solution's scalability, are outstanding. A good biological and agent design complemented with the locality model and the profit of agent's mobility makes this kind of applications feasible.