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A deep learning approach for the blind logP prediction in SAMPL6 challenge

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Abstract

Water octanol partition coefficient serves as a measure for the lipophilicity of a molecule and is important in the field of drug discovery. A novel method for computational prediction of logarithm of partition coefficient (logP) has been developed using molecular fingerprints and a deep neural network. The machine learning model was trained on a dataset of 12,000 molecules and tested on 2000 molecules. In this article, we present our results for the blind prediction of logP for the SAMPL6 challenge. While the best submission achieved a RMSE of 0.41 logP units, our submission had a RMSE of 0.61 logP units. Overall, we ranked in the top quarter out of the 92 submissions that were made. Our results show that the deep learning model can be used as a fast, accurate and robust method for high throughput prediction of logP of small molecules.

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Acknowledgements

Samarjeet would like to thank the Biochemistry, Cellular and Molecular Biology(BCMB) Program at JHU-SOM for supporting his graduate studies training. We would like to thank the LoBos and Biowulf teams at NIH for providing the high performance computing support to carry out the work. This study was supported by the Intramural Research Program of the National Heart, Lung and Blood Institute.

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Authors and Affiliations

  1. Biophysics and Biophysical Chemistry, The Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA

    Samarjeet Prasad

  2. Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20814, USA

    Samarjeet Prasad & Bernard R. Brooks

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  1. Samarjeet Prasad
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  2. Bernard R. Brooks
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Correspondence to Samarjeet Prasad.

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Prasad, S., Brooks, B.R. A deep learning approach for the blind logP prediction in SAMPL6 challenge. J Comput Aided Mol Des 34, 535–542 (2020). https://doi.org/10.1007/s10822-020-00292-3

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