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The interphase chromatin structure is extremely complex, precise and dynamic. Experimental methods can only show the frequency of interaction of the various parts of the chromatin. Therefore, it is extremely important to develop theoretical methods to predict the chromatin structure. In this publication, we implemented an extended version of the SBS model described by Barbieri et al. and created the ChroMC program that is easy to use and freely available (https://github.com/regulomics/chroMC) to other users. We also describe the necessary factors for the effective modeling of the chromatin structure in Drosophila melanogaster. We compared results of chromatin structure predictions using two methods: Monte Carlo and Molecular Dynamic. Our simulations suggest that incorporating black, non-reactive chromatin is necessary for successful prediction of chromatin structure, while the loop extrusion model with a …