PCP is a sofware that searches for cliques in the modified network, and merge cliques to form clusters using a “partial clique merging” method. Experiments show that (1) the use of indirect interactions and topological weight to augment protein-protein interactions can be used to improve the precision of clusters predicted by various existing clustering algorithms; and (2) our complex-finding algorithm performs very well on interaction networks modified in this way. Since no other information except the original PPI network is used, the would be very useful for protein complex prediction, especially for prediction of novel protein complexes.
DockStar is an algorithm for modeling of multimolecular protein complexes. It integrates both high resolution data of the individual subunits and low resolution data, such as the complex interaction graph and chemical cross-links.
Spotlight Web Service is designed to detect community structures in a network. Community, in which vertices are joined tightly together, between which there are only looser edges, exists in many real networks. Detecting community in a network is a very important research topic, because it has many practical applications. For example, detecting communities can help us find out real social groupings in a social network, related papers on a single topic in a citation network, protein complexes in Protein-Protein Interaction network, and web pages on related topics in the World Wide Web.
ProCope is a software package which provides easy access to different methods used for the prediction and evaluation of protein complexes from purification data experiments. 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.