In the construction of QSAR models for the prediction of molecular activity, feature selection is a common task aimed at improving the results and understanding of the problem. The selection of features allows elimination of irrelevant and redundant features, reduces the effect of dimensionality problems, and improves the generalization and interpretability of the models. In many feature selection applications, such as those based on ensembles of feature selectors, it is necessary to combine different selection processes. In this work, we evaluate the application of a new feature selection approach to the prediction of molecular activity, based on the construction of an undirected graph to combine base feature selectors. The experimental results demonstrate the efficiency of the graph-based method in terms of the classification performance, reduction, and redundancy compared to the standard voting method. The graph-based method can be extended to different feature selection algorithms and applied to other cheminformatics problems.