Journal
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
Volume 28, Issue 5, Pages 587-596Publisher
SPRINGER
DOI: 10.1007/s10822-014-9744-0
Keywords
Molecular lipophilicity potential; PyMOL; Virtual log P; Molecular docking; Hydrophobicity
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Funding
- Excellence scholarship of the University of Geneva, Switzerland
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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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