The DockOpt pipeline comprises predefined step sequences, which may be defined once and then reused. Thus DockOpt greatly simplifies benchmarking by facilitating the rigorous comparison of different DOCK parameterizations, DOCK executables, and even evaluation criteria. Moreover, different evaluation criteria can be applied in different steps within the same DockOpt pipeline, such as using a measure of enrichment first, followed by a measure of pose reproduction, and so on. Therefore, an entire experiment intended to measure the efficacy of several variables or search strategies can be defined in a single DockOpt pipeline and reproduced later simply by re-running the saved pipeline configuration.