Although none of the herein reported models was identified as the best performing one for all the 55 targets, our results suggested Morgan and RDK fingerprints as the best representations for the derivation of binary classifiers for the studied targets, particularly when derived using SVM, where no significative difference was found for their performance. This cannot be generalized for other, or even for these targets, since it could be associated with the hyperparameter space employed to optimize the models. Moreover, a model's performance is also dependent on the dataset composition, so the trends herein presented could change as more bioactivity data is published and different sets of hyperparameters are studied.