MesoBioNano Explorer (MBN Explorer) is a software package for the advanced multiscale simulations of complex molecular structure and dynamics, which is being developed and distributed in collaboration with the MBN Research Center gGmbH. MBN Explorer has many unique features and a wide range of applications in Physics, Chemistry, Biology, Material Science, and Industries. It is suitable for classical molecular dynamics (MD), irradiation-driven molecular dynamics (IDMD), Monte Carlo (MC), Euler and relativistic dynamics simulations of a large variety of molecular systems being in a solid, liquid or gaseous state. MBN Explorer includes a wide variety of interatomic potentials and allows the modeling of very different molecular systems, such as atomic clusters and nanoparticles, biomolecular systems, nanostructured materials, composite materials and materials interfaces, as well as to explore their thermo-mechanical properties, to simulate collision processes, and to provide valuable modelling support for novel and emerging technologies. MBN Explorer is available for all major operating systems (Windows, Linux, macOS) through the MBN Explorer official website https://mbnresearch.com/get-mbn-explorer-software.