Abstract—Identifying the binding partners of proteins is a problem of fundamental importance in computational biology. The PDZ is one of the most common and well-studied protein binding domains, hence it is a perfect model system for designing protein binding predictors. The standard approach to identifying the binding partners of PDZ domains uses multiple sequence alignments to infer the set of contact residues that are used in a predictive model. We expand on the sequence alignment approach by incorporating structural information to generate descriptors of the binding site geometry. Furthermore, we generate a real-value score for binary predictions by applying a filter based on models that predict the probability distributions of contact residues at each of the canonical PDZ ligand binding positions. Under training cross validation, our model produced an order of magnitude more predictions at a false positive proportion (FPP) of 10 percent than our benchmark model chosen from the literature. Evaluated using an independent cross validation, with computationally predicted structures, our model was able to make five times as many predictions as the benchmark model, with a Matthews' correlation coefficient (MCC) of 0.33. In addition, our model achieved a false positive proportion of 0.14, while the benchmark model had a 0.25 false positive proportion.