Abstract: The present subject matter relates to systems and methods for predicting molecular interactions within biological networks based on structural and non-structural indicators. Such molecules include but are not limited to proteins, nucleic acids and small molecules. In some embodiments, the present subject matter is directed to methods for predicting protein-protein interactions comprising obtaining a pair of query proteins, using sequence alignment to identify structural representatives for each of the pair of query proteins, and using structural alignment to determine sets of close and remote structural neighbors for each of the structural representatives. The method can include analyzing the close and remote structural neighbors to identify a reported complex, and using the reported complex to define a template for creating a model for interaction of the pair of query proteins.