Abstract: A drug IC50 deep learning model prediction method based on molecular structure and gene expression includes establishing a deep learning model to predict drug IC50 in different cell lines; predicting the drug IC50 in different cell lines based on the deep learning model. Also disclosed are prediction systems, electronic devices and computer readable storage media, which use grammar variational autoencoder to encode the chemical molecular formula of drugs and use autoencoder to encode cell line expression data, predict the drug IC50 in different cell lines through neural network methods, and predict the drug IC50 values of drugs in different types of cancer cell lines directly through the molecular information of drugs, which can reduce the investment of funds and time in preclinical development. Applying the model to patients helps screen out the applicable population of drugs, reduces unnecessary clinical trials, and improves the success rate of clinical trials.