Dataset Information

High-Throughput Discovery of Novel Cubic Crystal Materials Using Deep Generative Neural Networks.

ABSTRACT: High-throughput screening has become one of the major strategies for the discovery of novel functional materials. However, its effectiveness is severely limited by the lack of sufficient and diverse materials in current materials repositories such as the open quantum materials database (OQMD). Recent progress in deep learning have enabled generative strategies that learn implicit chemical rules for creating hypothetical materials with new compositions and structures. However, current materials generative models have difficulty in generating structurally diverse, chemically valid, and stable materials. Here we propose CubicGAN, a generative adversarial network (GAN) based deep neural network model for large scale generative design of novel cubic materials. When trained on 375 749 ternary materials from the OQMD database, the authors show that the model is able to not only rediscover most of the currently known cubic materials but also generate hypothetical materials of new structure prototypes. A total of 506 such materials have been verified by phonon dispersion calculation. Considering the importance of cubic materials in wide applications such as solar panels, the GAN model provides a promising approach to significantly expand existing materials repositories, enabling the discovery of new functional materials via screening. The new crystal structures discovered are freely accessible at www.carolinamatdb.org.

SUBMITTER: Zhao Y

PROVIDER: S-EPMC8529451 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature

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High-Throughput Discovery of Novel Cubic Crystal Materials Using Deep Generative Neural Networks.

Zhao Yong Y Al-Fahdi Mohammed M Hu Ming M Siriwardane Edirisuriya M D EMD Song Yuqi Y Nasiri Alireza A Hu Jianjun J

Advanced science (Weinheim, Baden-Wurttemberg, Germany) 20210805 20

High-throughput screening has become one of the major strategies for the discovery of novel functional materials. However, its effectiveness is severely limited by the lack of sufficient and diverse materials in current materials repositories such as the open quantum materials database (OQMD). Recent progress in deep learning have enabled generative strategies that learn implicit chemical rules for creating hypothetical materials with new compositions and structures. However, current materials g ...[more]

PMID: 34351707

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Project description:The discovery and development of novel pharmaceuticals is an area of active research mainly due to the large investments required and long payback times. As of 2016, the development of a novel drug candidate required up to $ USD 2.6 billion in investment for only 10% rate of approval by the FDA. To help decreasing the costs associated with the process, a number of in silico approaches have been developed with relatively low success due to limited predicting performance. Here, we introduced a machine learning-based algorithm as an alternative for a more accurate search of new pharmacological candidates, which takes advantage of Recurrent Neural Networks (RNN) for active molecule prediction within large databases. Our approach, termed PharmaNet was implemented here to search for ligands against specific cell receptors within 102 targets of the DUD-E database, which contains 22886 active molecules. PharmaNet comprises three main phases. First, a SMILES representation of the molecule is converted into a raw molecular image. Second, a convolutional encoder processes the data to obtain a fingerprint molecular image that is finally analyzed by a Recurrent Neural Network (RNN). This approach enables precise predictions of the molecules' target on the basis of the feature extraction, the sequence analysis and the relevant information filtered out throughout the process. Molecule Target prediction is a highly unbalanced detection problem and therefore, we propose that an adequate evaluation metric of performance is the area under the Normalized Average Precision (NAP) curve. PharmaNet largely surpasses the previous state-of-the-art method with 97.7% in the Receiver Operating Characteristic curve (ROC-AUC) and 65.5% in the NAP curve. We obtained a perfect performance for human farnesyl pyrophosphate synthase (FPPS), which is a potential target for antimicrobial and anticancer treatments. We decided to test PharmaNet for activity prediction against FPPS by searching in the CHEMBL data set. We obtained three (3) potential inhibitors that were further validated through both molecular docking and in silico toxicity prediction. Most importantly, one of this candidates, CHEMBL2007613, was predicted as a potential antiviral due to its involvement on the PCDH17 pathway, which has been reported to be related to viral infections.

Dataset Information

High-Throughput Discovery of Novel Cubic Crystal Materials Using Deep Generative Neural Networks.

Publications

High-Throughput Discovery of Novel Cubic Crystal Materials Using Deep Generative Neural Networks.

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