In this paper, a new approach to estimation problems of protein networks is proposed for systems biology. Generally, it is difficult to estimate complicated networks in molecular biology. In order to estimate complicated networks systematically, it is considered to estimate the networks based on system identification in control engineering. Considering that wave patterns of proteins are pseudo- periodic, the protein networks are estimated by the least- squares estimation method. In this method, the networks can be estimated by using just 1 cycle data of protein concentrations. Moreover, this method is applied to an estimation problem of protein networks for cell cycle in yeast, and 9-dimensional protein networks are actually estimated.