Gesellschaft für Informatik e.V.

Lecture Notes in Informatics

German Conference on Bioinformatics 2004, GCB 2004, October 4-6, 2004, Bielefeld, Germany P-53, 85-94 (2004).

GI, Gesellschaft für Informatik, Bonn


Robert Giegerich (ed.), Jens Stoye (ed.)

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Proteochemometrics modeling of receptor-ligand interactions using rough sets

Helena Stömbergsson , Peteris Prusis , Herman Midelfart , Jarl E. S. Wikberg and Jan Komorowski


We report on a model for the interaction of chimeric melanocortin G- protein coupled receptors with peptide ligands using the rough set approach. Rough sets generate If-Then rule models using Boolean reasoning. Two separate datasets have been analyzed, for which the binding affinities have previously been measured experimentally. The receptors and ligands are described by vectors of strings. Different partitions of each dataset were evaluated in order to find an optimal partition into rough set decision classes. To obtain a measurement of the accuracy of the rough set classifier generated from each dataset, a 10-fold cross validation (CV) was performed. The Area Under Curve (AUC) was calculated for each iteration during CV. This resulted in an AUC mean of 0.94 (SD 0.12) and 0.93 (SD 0.16) for the first and second dataset respectively. The CV results show

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GI, Gesellschaft für Informatik, Bonn
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