A method and system are provided for predicting chemical structures. The method includes receiving, at a user interface, intended structural feature values and intended chemical property values, as vectors. The method further includes constructing, by a hardware processor, a prediction model, wherein the prediction model predicts other structural feature values from the intended structural feature values and the intended chemical property values, and automatically configuring, by the hardware processor, at least one chemical structure candidate from the other structural feature vectors. The method additionally includes evaluating the at least one chemical structure candidate to determine structural feature values and chemical property values of the at least one chemical structure candidate and performing, by the hardware processor, machine learning of a chemical structure predicting system based on the evaluated structural feature values and the evaluated chemical property values of the at least one chemical structure candidate.