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MLP Tools: a PyMOL plugin for using the molecular lipophilicity potential in computer-aided drug design

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Abstract

The molecular lipophilicity potential (MLP) is a well-established method to calculate and visualize lipophilicity on molecules. We are here introducing a new computational tool named MLP Tools, written in the programming language Python, and conceived as a free plugin for the popular open source molecular viewer PyMOL. The plugin is divided into several sub-programs which allow the visualization of the MLP on molecular surfaces, as well as in three-dimensional space in order to analyze lipophilic properties of binding pockets. The sub-program Log MLP also implements the virtual log P which allows the prediction of the octanol/water partition coefficients on multiple three-dimensional conformations of the same molecule. An implementation on the recently introduced MLP GOLD procedure, improving the GOLD docking performance in hydrophobic pockets, is also part of the plugin. In this article, all functions of the MLP Tools will be described through a few chosen examples.

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Acknowledgments

The authors thank Dr. Antoine Daina for helpful preliminary discussion and the Excellence scholarship of the University of Geneva, Switzerland, for financial support.

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Authors and Affiliations

  1. School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Quai Ernest-Ansermet 30, 1211, Geneva 4, Switzerland

    Nils Oberhauser, Alessandra Nurisso & Pierre-Alain Carrupt

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  1. Nils Oberhauser
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  2. Alessandra Nurisso
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  3. Pierre-Alain Carrupt
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Corresponding author

Correspondence to Alessandra Nurisso.

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Oberhauser, N., Nurisso, A. & Carrupt, PA. MLP Tools: a PyMOL plugin for using the molecular lipophilicity potential in computer-aided drug design. J Comput Aided Mol Des 28, 587–596 (2014). https://doi.org/10.1007/s10822-014-9744-0

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  • DOI: https://doi.org/10.1007/s10822-014-9744-0

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