Recent advances in high-throughput technology have increased the quantity of available data on protein complexes and stimulated the development of many new prediction methods. In this article, we present ProCope, a Java software suite for the prediction and evaluation of protein complexes from affinity purification experiments which integrates the major methods for calculating interaction scores and predicting protein complexes published over the last years. Methods can be accessed via a graphical user interface, command line tools and a Java API. Using ProCope, existing algorithms can be applied quickly and reproducibly on new experimental results, individual steps of the different algorithms can be combined in new and innovative ways and new methods can be implemented and integrated in the existing prediction framework.