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Abstract Proteins and nucleic acids are key components in many processes in living cells, and interactions between proteins and nucleic acids are often crucial pathway components. In many cases, large flexibility of proteins as they interact with nucleic acids is key to their function. To understand the mechanisms of these processes, it is necessary to consider the 3D atomic structures of such protein–nucleic acid complexes. When such structures are not yet experimentally determined, protein docking can be used to computationally generate useful structure models. However, such docking has long had the limitation that the consideration of flexibility is usually limited to small movements or to small structures. We previously developed a method of flexible protein docking which could model ordered proteins which undergo large‐scale conformational changes, which we also showed was compatible with nucleic acids. Here, we elaborate on the ability of that pipeline, Flex‐LZerD, to model specifically interactions between proteins and nucleic acids, and demonstrate that Flex‐LZerD can model more interactions and types of conformational change than previously shown.