Suppr超能文献

生成化学:用深度学习生成模型进行药物发现。

Generative chemistry: drug discovery with deep learning generative models.

机构信息

Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA.

NIH National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA.

出版信息

J Mol Model. 2021 Feb 4;27(3):71. doi: 10.1007/s00894-021-04674-8.

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.

摘要

使用深度学习生成模型对分子结构进行从头设计,为药物发现带来了令人鼓舞的解决方案,有助于应对新药研发成本的不断增加。从原始文本、图像和视频的生成,到新颖分子结构的生成,深度学习生成模型的创造力展示了机器智能所能达到的高度。本文旨在综述基于生成模型来加速药物发现过程的生成化学的最新进展。本文从人工智能在药物发现领域的简要历史开始,概述了这一新兴范例。涵盖了化学信息学和机器学习中常用的化学数据库、分子表示和工具,作为生成化学的基础。详细讨论了如何利用先进的生成架构,包括递归神经网络、变分自动编码器、对抗自动编码器和生成对抗网络进行化合物生成。随后探讨了挑战和未来展望。

相似文献

1
Generative chemistry: drug discovery with deep learning generative models.
J Mol Model. 2021 Feb 4;27(3):71. doi: 10.1007/s00894-021-04674-8.
3
Data Integration Using Advances in Machine Learning in Drug Discovery and Molecular Biology.
Methods Mol Biol. 2021;2190:167-184. doi: 10.1007/978-1-0716-0826-5_7.
4
Navigating the frontier of drug-like chemical space with cutting-edge generative AI models.
Drug Discov Today. 2024 Sep;29(9):104133. doi: 10.1016/j.drudis.2024.104133. Epub 2024 Aug 3.
5
De Novo Peptide and Protein Design Using Generative Adversarial Networks: An Update.
J Chem Inf Model. 2022 Feb 28;62(4):761-774. doi: 10.1021/acs.jcim.1c01361. Epub 2022 Feb 7.
6
The power of deep learning to ligand-based novel drug discovery.
Expert Opin Drug Discov. 2020 Jul;15(7):755-764. doi: 10.1080/17460441.2020.1745183. Epub 2020 Mar 31.
7
Artificial intelligence to deep learning: machine intelligence approach for drug discovery.
Mol Divers. 2021 Aug;25(3):1315-1360. doi: 10.1007/s11030-021-10217-3. Epub 2021 Apr 12.
8
Generative machine learning for de novo drug discovery: A systematic review.
Comput Biol Med. 2022 Jun;145:105403. doi: 10.1016/j.compbiomed.2022.105403. Epub 2022 Mar 13.
10
Generative Deep Learning for Targeted Compound Design.
J Chem Inf Model. 2021 Nov 22;61(11):5343-5361. doi: 10.1021/acs.jcim.0c01496. Epub 2021 Oct 26.

引用本文的文献

1
Optimizing drug design by merging generative AI with a physics-based active learning framework.
Commun Chem. 2025 Aug 8;8(1):238. doi: 10.1038/s42004-025-01635-7.
2
Generative artificial intelligence based models optimization towards molecule design enhancement.
J Cheminform. 2025 Aug 4;17(1):116. doi: 10.1186/s13321-025-01059-4.
4
AI-Based Drug Discovery and Design for Different Genetic Designs.
Methods Mol Biol. 2025;2952:125-148. doi: 10.1007/978-1-0716-4690-8_8.
5
Capsule neural network and its applications in drug discovery.
iScience. 2025 Mar 14;28(4):112217. doi: 10.1016/j.isci.2025.112217. eCollection 2025 Apr 18.
6
A beginner's approach to deep learning applied to VS and MD techniques.
J Cheminform. 2025 Apr 8;17(1):47. doi: 10.1186/s13321-025-00985-7.
7
BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data.
Nucleic Acids Res. 2025 Jan 6;53(D1):D1633-D1644. doi: 10.1093/nar/gkae1075.
8
Hybrid deep learning technique for COX-2 inhibition bioactivity detection against breast cancer disease.
Biomed Eng Lett. 2024 Apr 10;14(4):631-647. doi: 10.1007/s13534-024-00355-6. eCollection 2024 Jul.
9
Navigating the complexity of p53-DNA binding: implications for cancer therapy.
Biophys Rev. 2024 Jul 11;16(4):479-496. doi: 10.1007/s12551-024-01207-4. eCollection 2024 Aug.

本文引用的文献

1
Advances and Perspectives in Applying Deep Learning for Drug Design and Discovery.
Front Robot AI. 2019 Nov 5;6:108. doi: 10.3389/frobt.2019.00108. eCollection 2019.
2
Mol-CycleGAN: a generative model for molecular optimization.
J Cheminform. 2020 Jan 8;12(1):2. doi: 10.1186/s13321-019-0404-1.
3
A de novo molecular generation method using latent vector based generative adversarial network.
J Cheminform. 2019 Dec 3;11(1):74. doi: 10.1186/s13321-019-0397-9.
4
High-Throughput Screening: today's biochemical and cell-based approaches.
Drug Discov Today. 2020 Oct;25(10):1807-1821. doi: 10.1016/j.drudis.2020.07.024. Epub 2020 Aug 12.
5
Pain-CKB, A Pain-Domain-Specific Chemogenomics Knowledgebase for Target Identification and Systems Pharmacology Research.
J Chem Inf Model. 2020 Oct 26;60(10):4429-4435. doi: 10.1021/acs.jcim.0c00633. Epub 2020 Sep 2.
6
Virus-CKB: an integrated bioinformatics platform and analysis resource for COVID-19 research.
Brief Bioinform. 2021 Mar 22;22(2):882-895. doi: 10.1093/bib/bbaa155.
7
Advances in G protein-coupled receptor high-throughput screening.
Curr Opin Biotechnol. 2020 Aug;64:210-217. doi: 10.1016/j.copbio.2020.06.004. Epub 2020 Jul 10.
8
Comparing Machine Learning Algorithms for Predicting Drug-Induced Liver Injury (DILI).
Mol Pharm. 2020 Jul 6;17(7):2628-2637. doi: 10.1021/acs.molpharmaceut.0c00326. Epub 2020 Jun 8.
9
Molecular Generation for Desired Transcriptome Changes With Adversarial Autoencoders.
Front Pharmacol. 2020 Apr 17;11:269. doi: 10.3389/fphar.2020.00269. eCollection 2020.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验