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In this paper an optimization framework is presented for automated performance-based seismic design of bridges consisting of multi-column RC pier substructures. The beneficial effects of fusing components on seismic performance of the quasi-isolated system is duly addressed in analysis and design. The proposed method is based on a two-step structural analysis consisting of a linear modal dynamic demand analysis and a nonlinear static capacity evaluation of the entire bridge structure. Results indicate that the proposed optimization method is capable of producing cost-effective design solutions combining the fusing behavior of bearings and yielding mechanism of piers. The optimal designs obtained from models addressing the performance of fusing components are far more efficient than those that do not take care of quasi-isolation behavior.