Protein-protein interactions are fundamental to cellular processes. Computational methods are useful for studying protein-protein interactions, but the majority of protein-protein docking software programs are limited to pairwise protein complexes. However, there are many other classes of protein complexes that are important to study, including multimeric protein complexes and disordered protein complexes. This dissertation introduces our computational method to model disordered protein complexes and presents our refinement of a method to predict the assembly order of multimeric protein complexes. Our research applies computational methods to a wider class of proteins than has been demonstrated previously. The methods developed in this work can be applied to obtain new biological insights into disordered protein complexes and multimeric complexes.