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Bioinformatics Vol. 19 no. 15 2003
pages 1901-1908
© 2003 Oxford University Press

A comprehensive set of protein complexes in yeast: mining large scale protein–protein interaction screens

Roland Krause 1,*, Christian von Mering 2 and Peer Bork 2

1 Cellzome AG, Meyerhofstraße 1, 69117 Heidelberg, Germany and 2 European Molecular Biology Laboratory, 69012 Heidelberg, Germany

Received on May 1, 2003 ; revised on July 15, 2003 ; accepted on July 15, 2003

Motivation: The analysis of protein–protein interactions allows for detailed exploration of the cellular machinery. The biochemical purification of protein complexes followed by identification of components by mass spectrometry is currently the method, which delivers the most reliable information—albeit that the data sets are still difficult to interpret.

Consolidating individual experiments into protein complexes, especially for high-throughput screens, is complicated by many contaminants, the occurrence of proteins in otherwise dissimilar purifications due to functional re-use and technical limitations in the detection. A non-redundant collection of protein complexes from experimental data would be useful for biological interpretation, but manual assembly is tedious and often inconsistent.

Results: Here, we introduce a measure to define similarity within collections of purifications and generate a set of minimally redundant, comprehensive complexes using unsupervised clustering.

Availability: Programs and results are freely available from http://www.bork.embl-heidelberg.de/Docu/purclust/

Contact: roland.krause{at}cellzome.com

* To whom correspondence should be addressed.


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