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Mannhold, R.* ; Poda, G.I.* ; Ostermann, C.* ; Tetko, I.V.

Calculation of molecular lipophilicity: State-of-the-art and comparison of log P methods on more than 96,000 compounds.

J. Pharm. Sci. 98, 861-893 (2009)
DOI
Open Access Green as soon as Postprint is submitted to ZB.
We first review the state-of-the-art in development of logP prediction approaches falling in two major categories: substructure-based and property-based methods. Then, we compare the predictive power of representative methods for one public (N=266) and two in House datasets from Nycomed (N=882) and Pfizer (N=95809). A total of 30 methods were tested for public and industrial datasets, respectively. Accuracy of models declined with the number of nonhydrogen atoms. The Arithmetic Average Model (AAM), which predicts the same value (the arithmetic mean) for all compounds, was used as a baseline model for comparison. Methods with Root Mean Squared Error (RMSE) greater than RMSE produced by the AAM were considered as unacceptable. The majority of analyzed methods produced reasonable results for the public dataset but only seven methods were successful on the both in house datasets. We proposed a simple equation based on the number of carbon atoms, NC, and the number of hetero atoms, NHET: logP=1.46(+/- 0.02) +0.11(+/-0.001) NC-0.11 (+/- 0.001) NHET. This equation outperformed a large number of programs benchmarked in this study. Factors influencing the accuracy of log P predictions were elucidated and discussed. 2008 Willey-Liss, Inc. and the American Pharmacists Association J Pharm Sci.
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords lipophilicity; log P calculation; substructure-based approaches; fragmental methods; atom-based methods; property-based approaches; methods based on 3D-structure representation; empirical approaches; quantum chemical semi-empirical calculations; continuum
ISSN (print) / ISBN 0022-3549
e-ISSN 1520-6017
Conference Title State-of-the-Art and Comparison of Log P Methods on More Than 96,000 Compounds
Journal Journal of Pharmaceutical Sciences
Quellenangaben Volume: 98, Issue: 3, Pages: 861-893 Article Number: , Supplement: ,
Publisher Wiley
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Institute of Bioinformatics and Systems Biology (IBIS)