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Bioinformatics Advance Access originally published online on October 4, 2005
Bioinformatics 2005 21(23):4289-4296; 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{at}oxfordjournals.org
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

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

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

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

*To whom correspondence should be addressed.

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 datasets 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.

Contact: jarl.wikberg{at}farmbio.uu.se

Supplementary information: Supplementary data are available at Bioinformatics online.

Received on June 23, 2005; revised on September 20, 2005; accepted on October 3, 2005

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