Literature DB >> 33543405

Generative chemistry: drug discovery with deep learning generative models.

Yuemin Bian1,2, Xiang-Qun Xie3,4,5,6.   

Abstract

The de novo design of molecular structures using deep learning generative models introduces an encouraging solution to drug discovery in the face of the continuously increased cost of new drug development. From the generation of original texts, images, and videos, to the scratching of novel molecular structures the creativity of deep learning generative models exhibits the height machine intelligence can achieve. The purpose of this paper is to review the latest advances in generative chemistry which relies on generative modeling to expedite the drug discovery process. This review starts with a brief history of artificial intelligence in drug discovery to outline this emerging paradigm. Commonly used chemical databases, molecular representations, and tools in cheminformatics and machine learning are covered as the infrastructure for generative chemistry. The detailed discussions on utilizing cutting-edge generative architectures, including recurrent neural network, variational autoencoder, adversarial autoencoder, and generative adversarial network for compound generation are focused. Challenges and future perspectives follow.

Keywords:  Adversarial autoencoder; Deep learning; Drug discovery; Generative adversarial network; Generative model; Recurrent neural network; Variational autoencoder

Year:  2021        PMID: 33543405     DOI: 10.1007/s00894-021-04674-8

Source DB:  PubMed          Journal:  J Mol Model        ISSN: 0948-5023            Impact factor:   1.810


  65 in total

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Journal:  Curr Protein Pept Sci       Date:  2007-08       Impact factor: 3.272

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Journal:  Nature       Date:  1996-11-07       Impact factor: 49.962

Review 5.  Software for molecular docking: a review.

Authors:  Nataraj S Pagadala; Khajamohiddin Syed; Jack Tuszynski
Journal:  Biophys Rev       Date:  2017-01-16

6.  Integrated In Silico Fragment-Based Drug Design: Case Study with Allosteric Modulators on Metabotropic Glutamate Receptor 5.

Authors:  Yuemin Bian; Zhiwei Feng; Peng Yang; Xiang-Qun Xie
Journal:  AAPS J       Date:  2017-05-30       Impact factor: 4.009

7.  CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.

Authors:  K Vanommeslaeghe; E Hatcher; C Acharya; S Kundu; S Zhong; J Shim; E Darian; O Guvench; P Lopes; I Vorobyov; A D Mackerell
Journal:  J Comput Chem       Date:  2010-03       Impact factor: 3.376

Review 8.  Advances in G protein-coupled receptor high-throughput screening.

Authors:  Emily A Yasi; Nicholas S Kruyer; Pamela Peralta-Yahya
Journal:  Curr Opin Biotechnol       Date:  2020-07-10       Impact factor: 9.740

9.  Estimated Research and Development Investment Needed to Bring a New Medicine to Market, 2009-2018.

Authors:  Olivier J Wouters; Martin McKee; Jeroen Luyten
Journal:  JAMA       Date:  2020-03-03       Impact factor: 157.335

10.  Computational systems pharmacology analysis of cannabidiol: a combination of chemogenomics-knowledgebase network analysis and integrated in silico modeling and simulation.

Authors:  Yue-Min Bian; Xi-Bing He; Yan-Kang Jing; Li-Rong Wang; Jun-Mei Wang; Xiang-Qun Xie
Journal:  Acta Pharmacol Sin       Date:  2018-09-10       Impact factor: 6.150

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  4 in total

1.  Artificial Intelligent Deep Learning Molecular Generative Modeling of Scaffold-Focused and Cannabinoid CB2 Target-Specific Small-Molecule Sublibraries.

Authors:  Yuemin Bian; Xiang-Qun Xie
Journal:  Cells       Date:  2022-03-07       Impact factor: 6.600

2.  DenovoProfiling: A webserver for de novo generated molecule library profiling.

Authors:  Zhihong Liu; Jiewen Du; Ziying Lin; Ze Li; Bingdong Liu; Zongbin Cui; Jiansong Fang; Liwei Xie
Journal:  Comput Struct Biotechnol J       Date:  2022-08-02       Impact factor: 6.155

3.  Machine Learning Guided Discovery of Non-Hemolytic Membrane Disruptive Anticancer Peptides.

Authors:  Elena Zakharova; Markus Orsi; Alice Capecchi; Jean-Louis Reymond
Journal:  ChemMedChem       Date:  2022-08-05       Impact factor: 3.540

4.  Machine learning designs non-hemolytic antimicrobial peptides.

Authors:  Alice Capecchi; Xingguang Cai; Hippolyte Personne; Thilo Köhler; Christian van Delden; Jean-Louis Reymond
Journal:  Chem Sci       Date:  2021-06-07       Impact factor: 9.825

  4 in total

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