title: ProCope--protein complex prediction and evaluation.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  Source code and executables are available at http://www.bio.ifi.lmu.de/Complexes/ProCope/.
authors.affiliation: Institut für Informatik, Ludwig-Maximilians-Universität München, Amalienstrasse 17, 80333 München, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Krumsiek
authors.forename: Caroline C
authors.initials: CC
authors.lastname: Friedel
authors.forename: Ralf
authors.initials: R
authors.lastname: Zimmer
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D008954:Models, Biological; D046912:Multiprotein Complexes / Q000032:analysis*; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012984:Software; D014584:User-Computer Interface
chemical_list: D046912:Multiprotein Complexes