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MBN Explorer allows to use a broad variety of interatomic potentials, to model different molecular systems, such as atomic clusters, fullerenes, nanotubes, polypeptides, proteins, DNA, composite systems, nanofractals, and so on. A distinct feature of the program, which makes it significantly different from the existing codes, is its universality and applicability to the description of a broad range of problems involving different molecular systems. Most of the existing codes are developed for particular classes of molecular systems and do not permit multiscale approach while MBN Explorer goes beyond these drawbacks. On demand, MBN Explorer allows to group particles in the system into rigid fragments, thereby significantly reducing the number of dynamical degrees of freedom. 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