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机器学习在药理学和 ADMET 终点建模中的应用。

Machine Learning Applied to the Modeling of Pharmacological and ADMET Endpoints.

机构信息

Pharmaceuticals, Research and Development, Computational Molecular Design, Bayer AG, Wuppertal, Germany.

Pharmaceuticals, Research and Development, Computational Molecular Design, Bayer AG, Berlin, Germany.

出版信息

Methods Mol Biol. 2022;2390:61-101. doi: 10.1007/978-1-0716-1787-8_2.

DOI:10.1007/978-1-0716-1787-8_2
PMID:34731464
Abstract

The well-known concept of quantitative structure-activity relationships (QSAR) has been gaining significant interest in the recent years. Data, descriptors, and algorithms are the main pillars to build useful models that support more efficient drug discovery processes with in silico methods. Significant advances in all three areas are the reason for the regained interest in these models. In this book chapter we review various machine learning (ML) approaches that make use of measured in vitro/in vivo data of many compounds. We put these in context with other digital drug discovery methods and present some application examples.

摘要

近年来,定量构效关系(QSAR)这一广为人知的概念引起了人们的浓厚兴趣。数据、描述符和算法是构建有用模型的主要支柱,这些模型支持通过计算方法更有效地进行药物发现。这三个领域的显著进展是这些模型重新受到关注的原因。在本章中,我们回顾了各种机器学习(ML)方法,这些方法利用了许多化合物的体外/体内测量数据。我们将这些方法与其他数字药物发现方法进行了比较,并介绍了一些应用实例。

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Machine Learning Applied to the Modeling of Pharmacological and ADMET Endpoints.机器学习在药理学和 ADMET 终点建模中的应用。
Methods Mol Biol. 2022;2390:61-101. doi: 10.1007/978-1-0716-1787-8_2.
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Machine Learning for In Silico ADMET Prediction.基于机器学习的计算机辅助药物代谢动力学预测。
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本文引用的文献

1
Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects.大规模评估结合自由能计算在药物研发项目中的应用。
J Chem Inf Model. 2020 Nov 23;60(11):5457-5474. doi: 10.1021/acs.jcim.0c00900. Epub 2020 Sep 3.
2
Impact of Protein Preparation on Resulting Accuracy of FEP Calculations.蛋白质制备对 FEP 计算结果准确性的影响。
J Chem Inf Model. 2020 Nov 23;60(11):5287-5289. doi: 10.1021/acs.jcim.0c00445. Epub 2020 Aug 2.
3
Bayer's in silico ADMET platform: a journey of machine learning over the past two decades.
拜耳公司的计算机辅助药物设计(ADMET)平台:机器学习在过去二十年中的发展历程。
Drug Discov Today. 2020 Sep;25(9):1702-1709. doi: 10.1016/j.drudis.2020.07.001. Epub 2020 Jul 9.
4
Chemoproteomic Profiling of a Pharmacophore-Focused Chemical Library.基于药效团的化学文库的化学生物学蛋白质组学分析
Cell Chem Biol. 2020 Jun 18;27(6):708-718.e10. doi: 10.1016/j.chembiol.2020.04.007. Epub 2020 May 12.
5
QSAR without borders.无边界定量构效关系。
Chem Soc Rev. 2020 Jun 7;49(11):3525-3564. doi: 10.1039/d0cs00098a. Epub 2020 May 1.
6
Improvement in ADMET Prediction with Multitask Deep Featurization.多任务深度特征化提高 ADMET 预测
J Med Chem. 2020 Aug 27;63(16):8835-8848. doi: 10.1021/acs.jmedchem.9b02187. Epub 2020 May 12.
7
Prediction of Oral Bioavailability in Rats: Transferring Insights from in Vitro Correlations to (Deep) Machine Learning Models Using in Silico Model Outputs and Chemical Structure Parameters.大鼠口服生物利用度预测:通过体内外相关性和(深度)机器学习模型,利用计算模型输出和化学结构参数进行转移。
J Chem Inf Model. 2019 Nov 25;59(11):4893-4905. doi: 10.1021/acs.jcim.9b00460. Epub 2019 Nov 12.
8
BRADSHAW: a system for automated molecular design.BRADSHAW:一个自动化分子设计系统。
J Comput Aided Mol Des. 2020 Jul;34(7):747-765. doi: 10.1007/s10822-019-00234-8. Epub 2019 Oct 21.
9
Addressing the Challenge of Polypharmacy.应对多重用药挑战。
Annu Rev Pharmacol Toxicol. 2020 Jan 6;60:661-681. doi: 10.1146/annurev-pharmtox-010919-023508. Epub 2019 Oct 7.
10
Reaction-Based Enumeration, Active Learning, and Free Energy Calculations To Rapidly Explore Synthetically Tractable Chemical Space and Optimize Potency of Cyclin-Dependent Kinase 2 Inhibitors.基于反应的枚举、主动学习和自由能计算,快速探索合成上可处理的化学空间并优化细胞周期蛋白依赖性激酶 2 抑制剂的效力。
J Chem Inf Model. 2019 Sep 23;59(9):3782-3793. doi: 10.1021/acs.jcim.9b00367. Epub 2019 Aug 22.