The discrimination of protein-protein complexes in transient and permanent complexes is of great interest when it comes to shedding light on various regulatory pathways.The analysis of available datasets in this field reveals that they are often biased towards homodimeric permanent and heterodimeric transient protein-protein interactions. Consequently, most methods derive descriptors to discriminate between homo- and heterodimers. However, the real challenge is the discrimination of permanent from transient heterodimers.We calculated several characteristics of protein-protein interactions and analyzed diverse descriptor variations by means of a SVM. The hydrophobic binding energy and the proportion of the interface ratios arose as most promising descriptors. Contrary to many other methods, which employ numerous complicated descriptors, we only use these two intuitive ones. Our model achieves comparable accuracies of 92.5% in the training set and 77.1% on an independent set. Using the hydrophobic energy as only descriptor, 80.2% of the permanent and transient heterodimers are correctly predicted1. A web server is available: http://ppi.zbh.uni-hamburg.de  References: 1.  E. Vennmann, N. Schneider, G. Lange, M. Rarey, 2011 , submitted

Discrimination of permanent and transient heterodimers: A real challenge in the classification of protein-protein interactions

243rd National Meeting (2012)

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