Protein-protein interactions play a crucial role in almost all cellular processes . Identifying interacting proteins reveals insight into living organisms and yields novel drug targets for disease treatment . Here, we present a publicly available, automated pipeline to predict genome-wide protein-protein interactions and produce high-quality multimeric structural models . Application of our method to the Human and Yeast genomes yield protein-protein interaction networks similar in quality to common experimental methods . We identified and modeled Human proteins likely to interact with the papain-like protease of SARS-CoV2 ’ s non-structural protein 3 (Nsp3). We also produced models of SARS-CoV2 ’ s spike protein (S) interacting with myelin-oligodendrocyte glycoprotein receptor (MOG) and dipeptidyl peptidase-4 (DPP4). The presented method is capable of confidently identifying interactions while providing high-quality multimeric structural models for experimental validation . The interactome modeling pipeline is available at usegalaxy.org.