This paper proposes an estimation problem of protein networks for cell cycle and their robustness analysis. Our proposed method is explained to estimate a protein network for cell cycle based on system identification techniques. The method is based on the least-squares method for state space models. Applying the method, a 6-dimensional protein network is estimated for cell cycle to demonstrate the efficacy of our proposed method. The estimated protein network is called as 6-dimensional cell cycle system and the cell cycle system is described as nonlinear differential equations. Moreover robustness analysis and numerical simulations are performed for the cell cycle system described as nonlinear differential equations. From these results, robustness of the cell cycle system is discussed.