We introduce a Computational Fluid Dynamics (CFD) based method for performing patient-specific coronary hemodynamic computations under two conditions: at rest and during drug-induced hyperemia. The proposed method is based on a novel estimation procedure for determining the boundary conditions from non-invasively acquired patient data at rest. A multi-variable feedback control framework ensures that the computed mean arterial pressure and the flow distribution matches the estimated values for an individual patient during the rest state. The boundary conditions at hyperemia are derived from the respective rest-state values via a transfer function that models the vasodilation phenomenon. Simulations are performed on a coronary tree where a 65% diameter stenosis is introduced in the left anterior descending (LAD) artery, with the boundary conditions estimated using the proposed method. The results demonstrate that the estimation of the hyperemic resistances is crucial in order to obtain accurate values for pressure and flow rates. Results from an exhaustive sensitivity analysis have been presented for analyzing the variability of trans-stenotic pressure drop and Fractional Flow Reserve (FFR) values with respect to various measurements and assumptions.