A novel methodology for the modeling and characterization of the enzymatic hydrolysis of proteins is proposed. The hydrolysis time course can be predicted at different operating conditions for protein concentration, enzyme concentration and temperature. The hydrolysis kinetics of salmon muscle proteins and whey protein isolate by Alcalase were studied using a central composite design. A combination of the logarithmic equation P=1/bIn (abt+1) to model the hydrolysis time course with the response surface methodology to correlate the kinetic constants a and b with the operating conditions: protein concentration, enzyme concentration and temperature were achieved. The logarithmic equation was a very good fit with the hydrolysis time courses, with both substrates achieving R-2>0.995. The kinetic constants a and b were significantly affected by the operating conditions. Empirical models were obtained for a and b as functions of operating conditions. The kinetic constant values were predicted, and a strong correlation between predicted and experimental values was obtained for a (R-2=0.949) and b (R-2=0.945). The predicted and experimental time courses resulted in good correlation for both salmon muscle proteins (R-2>0.987) and whey protein isolate (R-2>0.978). The model allowed calculation of the hydrolysis time course of proteins from a given set of operating conditions with good predictability. This methodology can be used with different sources of proteins and enzymes to test the susceptibility of proteins to hydrolysis as well as the catalytic efficiency of proteases. Additionally, the combined model can be used as a design and optimization function. (C) 2015 Elsevier Ltd. All rights reserved.