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Chemi-Net: A Molecular Graph Convolutional Network for Accurate Drug Property Prediction

1
Accutar Biotechnology Inc., 760 Parkside Ave., Brooklyn, NY 11226, USA
2
Amgen Inc., 1 Amgen Center Dr., Thousand Oaks, CA 91320, USA
3
Amgen Inc., 360 Binney St., Cambridge, MA 02141, USA
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Int. J. Mol. Sci. 2019, 20(14), 3389; https://doi.org/10.3390/ijms20143389
Received: 22 March 2019 / Revised: 10 June 2019 / Accepted: 2 July 2019 / Published: 10 July 2019
(This article belongs to the Special Issue Artificial Intelligence and Computer Aided Drug Design)
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Abstract

Absorption, distribution, metabolism, and excretion (ADME) studies are critical for drug discovery. Conventionally, these tasks, together with other chemical property predictions, rely on domain-specific feature descriptors, or fingerprints. Following the recent success of neural networks, we developed Chemi-Net, a completely data-driven, domain knowledge-free, deep learning method for ADME property prediction. To compare the relative performance of Chemi-Net with Cubist, one of the popular machine learning programs used by Amgen, a large-scale ADME property prediction study was performed on-site at Amgen. For all 13 data sets, Chemi-Net resulted in higher R2 values compared with the Cubist benchmark. The median R2 increase rate over Cubist was 26.7%. We expect that the significantly increased accuracy of ADME prediction seen with Chemi-Net over Cubist will greatly accelerate drug discovery. View Full-Text
Keywords: deep learning; ADME prediction; drug discovery deep learning; ADME prediction; drug discovery
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Liu, K.; Sun, X.; Jia, L.; Ma, J.; Xing, H.; Wu, J.; Gao, H.; Sun, Y.; Boulnois, F.; Fan, J. Chemi-Net: A Molecular Graph Convolutional Network for Accurate Drug Property Prediction. Int. J. Mol. Sci. 2019, 20, 3389.

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