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Recent studies have demonstrated the benefits of using fractional derivatives to simulate a blood pressure profile. In this work we propose to combine a one-dimensional model of coronary blood flow with fractional-order Windkessel boundary conditions. This allows us to obtain a greater variety of blood pressure profiles for better model personalization An algorithm of parameter identification is described, which is used to fit the measured mean value of arterial pressure and estimate the fractional flow reserve (FFR) for a given patient. The proposed framework is used to investigate sensitivity of mean blood pressure and fractional flow reserve to fractional order. We demonstrate that the fractional derivative order significantly affects the fractional flow reserve (FFR), which is used as an indicator of stenosis significance.