Objective. The objective of this study is to develop a multi-scale modeling approach that accurately predicts radiation-induced DNA damage and survival fraction in specific cell lines.Approach. A Monte Carlo based simulation framework was employed to make the predictions. The FLUKA Monte Carlo code was utilized to estimate absorbed doses and fluence energy spectra, which were then used in the Monte Carlo Damage Simulation code to compute DNA damage yields in Chinese hamster V79 cell lines. The outputs were converted into cell survival fractions using a previously published theoretical model. To reduce the uncertainties of the predictions, new values for the parameters of the theoretical model were computed, expanding the database of experimental points considered in the previous estimation. Simulated results were validated against experimental data, confirming the applicability of the framework for proton beams up to 230 MeV. Additionally, the impact of secondary particles on cell survival was estimated.Main results. The simulated survival fraction versus depth in a glycerol phantom is reported for eighteen different configurations. Two proton spread out Bragg peaks at several doses were simulated and compared with experimental data. In all cases, the simulations follow the experimental trends, demonstrating the accuracy of the predictions up to 230 MeV.Significance. This study holds significant importance as it contributes to the advancement of models for predicting biological responses to radiation, ultimately contributing to more effective cancer treatment in proton therapy.