Provided are a method and an apparatus for analyzing a relation between a drug and a protein. Further, the present invention relates to drug repositioning. The method for analyzing a relation between a drug and a protein may include a protein location information inputting step of receiving protein location information representing a location where the protein included in a training data set is present in a cell, with regard to the training data set including at least one combination data of the drug and the protein having interrelation; and a classifier training step of training the classifier for determining a correlation between the drug and the protein by using the training data set based on protein feature information of the protein including the protein location information and drug feature information of the drug.
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