The article discusses methods of building frame constructions modeling by finite element method, taking into account seismic isolation systems. It presents data of the calculation in the two software systems. The calculation results are compared by analyzing of the individual elements stress-strain state. Recommendations about the calculation schemes and software systems selection are given on the base of results analyzing. The achieved results allow us to evaluate the effectiveness of seismic base isolation and can be used for wide application of such systems in building area.