3D Molecular Representations Based on the Wave Transform for Convolutional Neural Networks

Molecular Pharmaceutics
Denis KuzminykhAlex Zhavoronkov

Abstract

Convolutional neural networks (CNN) have been successfully used to handle three-dimensional data and are a natural match for data with spatial structure such as 3D molecular structures. However, a direct 3D representation of a molecule with atoms localized at voxels is too sparse, which leads to poor performance of the CNNs. In this work, we present a novel approach where atoms are extended to fill other nearby voxels with a transformation based on the wave transform. Experimenting on 4.5 million molecules from the Zinc database, we show that our proposed representation leads to better performance of CNN-based autoencoders than either the voxel-based representation or the previously used Gaussian blur of atoms and then successfully apply the new representation to classification tasks such as MACCS fingerprint prediction.

References

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Mar 24, 2016·Molecular Pharmaceutics·Polina MamoshinaAlex Zhavoronkov
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Citations

Jun 4, 2019·Briefings in Bioinformatics·Mengying SunFei Wang
Jan 21, 2020·Clinical Pharmacology and Therapeutics·Alex ZhavoronkovTudor I Oprea
Sep 4, 2019·Nature Biotechnology·Alex ZhavoronkovAlán Aspuru-Guzik
Mar 7, 2020·Science Advances·Benjamin AlldrittAdam S Foster
Apr 2, 2020·Expert Opinion on Drug Discovery·Igor I Baskin
May 5, 2020·Frontiers in Pharmacology·Rim ShayakhmetovDaniil Polykovskiy
Aug 6, 2020·The Journal of Chemical Physics·Mads-Peter V ChristiansenBjørk Hammer
Aug 15, 2018·International Journal of Molecular Sciences·Yunyi Wu, Guanyu Wang
Feb 15, 2021·Journal of Computational Chemistry·Maksym DruchokMykola Maksymenko
Mar 1, 2021·Journal of Molecular Graphics & Modelling·Qinqing LiuMinghu Song
Mar 24, 2021·Journal of Chemical Information and Modeling·Derek JonesJonathan E Allen
Jul 6, 2020·Current Topics in Medicinal Chemistry·Ravina KhandelwalSanjeev Kumar Singh
Apr 27, 2021·Journal of Chemical Information and Modeling·Phan NguyenT Yong-Jin Han
Jun 3, 2021·Expert Opinion on Drug Discovery·Fabio BonioloMichael P Menden
Sep 29, 2020·Journal of Chemical Information and Modeling·Jacques BoitreaudJérôme Waldispühl
Aug 25, 2020·ACS Medicinal Chemistry Letters·Quentin VanhaelenAlex Zhavoronkov
Jul 13, 2018·Molecular Pharmaceutics·Yoni DonnerKristen Fortney
Aug 1, 2018·Molecular Pharmaceutics·Shahar Harel, Kira Radinsky
Sep 6, 2018·Molecular Pharmaceutics·Daniil PolykovskiyArtur Kadurin
Apr 12, 2019·Journal of Chemical Information and Modeling·Wesley Beckner, Jim Pfaendtner
Feb 13, 2020·Journal of Chemical Information and Modeling·Jocelyn Sunseri, David R Koes
Jul 16, 2019·The Journal of Physical Chemistry Letters·Shuai LiuTeresa Head-Gordon
Sep 10, 2021·Briefings in Bioinformatics·María Virginia SabandoAxel J Soto

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