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Bioinformatics Advance Access originally published online on July 17, 2008
Bioinformatics 2008 24(18):2115-2116; doi:10.1093/bioinformatics/btn376
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

ProCope—protein complex prediction and evaluation

Jan Krumsiek , Caroline C. Friedel * and Ralf Zimmer

Institut für Informatik, Ludwig-Maximilians-Universität München, Amalienstraße 17, 80333 München, Germany

*To whom correspondence should be addressed.


  Abstract

Summary: 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.

Availability: Source code and executables are available at http://www.bio.ifi.lmu.de/Complexes/ProCope/

Contact: Caroline.Friedel{at}bio.ifi.lmu.de

Associate Editor: Burkhard Rost

Received on May 27, 2008; revised on July 7, 2008; accepted on July 15, 2008

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C. C. Friedel and R. Zimmer
Identifying the topology of protein complexes from affinity purification assays
Bioinformatics, August 15, 2009; 25(16): 2140 - 2146.
[Abstract] [Full Text] [PDF]


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