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Bioinformatics Advance Access published online on October 4, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti703
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received June 23, 2005
Revised September 20, 2005
Accepted October 3, 2005

Article

Improved approach for proteochemometrics modeling: application to organic compound - amine G protein-coupled receptor interactions

Maris Lapinsh 1, Peteris Prusis 1, Staffan Uhlén 1, and Jarl E. S. Wikberg 1*

1 Department of Pharmaceutical Biosciences, Uppsala University, Box 591 BMC, SE-751 24 Uppsala, Sweden


  Abstract

Motivation: Proteochemometrics is a novel technology for the analysis of interactions of series of proteins with series of ligands. We have here customized it for analysis of large data sets and evaluated it for the modeling of the interaction of psychoactive organic amines with all the five known families of amine G protein-coupled receptors (GPCRs).

Results: The model exploited data for the binding of 22 compounds to 31 amine GPCRs, correlating chemical descriptions and cross-descriptions of compounds and receptors to binding affinity using a novel strategy. A highly valid model (q2=0.76) was obtained which was further validated by external predictions using data for 10 other entirely independent compounds, yielding the high q2ext=0.67. Interpretation of the model reveals molecular interactions that govern psychoactive organic amines overall affinity for amine GPCRs, as well as their selectivity for particular amine GPCRs. The new modeling procedure allows us to obtain fully interpretable proteochemometrics models using essentially unlimited number of ligand and protein descriptors.


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