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SAMPL6 logP challenge: machine learning and quantum mechanical approaches

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Abstract

Two different types of approaches: (a) approaches that combine quantitative structure activity relationships, quantum mechanical electronic structure methods, and machine-learning and, (b) electronic structure vertical solvation approaches, were used to predict the logP coefficients of 11 molecules as part of the SAMPL6 logP blind prediction challenge. Using electronic structures optimized with density functional theory (DFT), several molecular descriptors were calculated for each molecule, including van der Waals areas and volumes, HOMO/LUMO energies, dipole moments, polarizabilities, and electrophilic and nucleophilic superdelocalizabilities. A multilinear regression model and a partial least squares model were used to train a set of 97 molecules. As well, descriptors were generated using the molecular operating environment and used to create additional machine learning models. Electronic structure vertical solvation approaches considered include DFT and the domain-based local pair natural orbital methods combined with the solvated variant of the correlation consistent composite approach.

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Acknowledgements

The authors gratefully acknowledge the University of North Texas Academic Computing Services for the use of the UNT Research Clusters. Computational resources were provided via the NSF Major Research Instrumentation program supported by the National Science Foundation under Grant No. CHE-1531468. This research was supported in part by the Intermural Research Program of the National Heart, Lung, and Blood Institute of the National Institutes of Health and utilized the high-performance computational capabilities of the LoBoS and Biowulf Linux clusters at the National Institutes of Health (http://www.lobos.nih.gov and http://biowulf.nih.gov).

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Authors and Affiliations

  1. Department of Chemistry, Michigan State University, East Lansing, MI, 48824-1322, USA

    Prajay Patel & Angela K. Wilson

  2. Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, TX, 76203-5070, USA

    David M. Kuntz & Angela K. Wilson

  3. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20852-5690, USA

    Michael R. Jones & Bernard R. Brooks

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  1. Prajay Patel
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Correspondence to Angela K. Wilson.

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Patel, P., Kuntz, D.M., Jones, M.R. et al. SAMPL6 logP challenge: machine learning and quantum mechanical approaches. J Comput Aided Mol Des 34, 495–510 (2020). https://doi.org/10.1007/s10822-020-00287-0

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