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计算机辅助药物设计:更新。

Computer-Aided Drug Design: An Update.

机构信息

Department of Pharmaceutical Sciences, Computer-Aided Drug Design Center, School of Pharmacy, University of Maryland, Baltimore, MD, USA.

Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD, USA.

出版信息

Methods Mol Biol. 2023;2601:123-152. doi: 10.1007/978-1-0716-2855-3_7.

Abstract

Computer-aided drug design (CADD) approaches are playing an increasingly important role in understanding the fundamentals of ligand-receptor interactions and helping medicinal chemists design therapeutics. About 5 years ago, we presented a chapter devoted to an overview of CADD methods and covered typical CADD protocols including structure-based drug design (SBDD) and ligand-based drug design (LBDD) approaches that were frequently used in the antibiotic drug design process. Advances in computational hardware and algorithms and emerging CADD methods are enhancing the accuracy and ability of CADD in drug design and development. In this chapter, an update to our previous chapter is provided with a focus on new CADD approaches from our laboratory and other peers that can be employed to facilitate the development of antibiotic therapeutics.

摘要

计算机辅助药物设计(CADD)方法在理解配体-受体相互作用的基本原理和帮助药物化学家设计治疗药物方面发挥着越来越重要的作用。大约 5 年前,我们发表了一章专门介绍 CADD 方法的概述,涵盖了典型的 CADD 方案,包括经常用于抗生素药物设计过程的基于结构的药物设计(SBDD)和基于配体的药物设计(LBDD)方法。计算硬件和算法的进步以及新兴的 CADD 方法正在提高 CADD 在药物设计和开发中的准确性和能力。在本章中,我们对上一章进行了更新,重点介绍了我们实验室和其他同行的新 CADD 方法,这些方法可用于促进抗生素治疗药物的开发。

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1
Application of Site-Identification by Ligand Competitive Saturation in Computer-Aided Drug Design.
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2
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3
CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field.
J Comput Chem. 2022 Feb 15;43(5):359-375. doi: 10.1002/jcc.26795. Epub 2021 Dec 7.
5
Druggable Allosteric Sites in β-Propeller Lectins.
Angew Chem Int Ed Engl. 2022 Jan 3;61(1):e202109339. doi: 10.1002/anie.202109339. Epub 2021 Nov 23.
6
SeamDock: An Interactive and Collaborative Online Docking Resource to Assist Small Compound Molecular Docking.
Front Mol Biosci. 2021 Sep 17;8:716466. doi: 10.3389/fmolb.2021.716466. eCollection 2021.
7
A practical guide to large-scale docking.
Nat Protoc. 2021 Oct;16(10):4799-4832. doi: 10.1038/s41596-021-00597-z. Epub 2021 Sep 24.
8
Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field.
J Chem Theory Comput. 2021 Oct 12;17(10):6262-6280. doi: 10.1021/acs.jctc.1c00571. Epub 2021 Sep 22.
9
Accelerating antibiotic discovery through artificial intelligence.
Commun Biol. 2021 Sep 9;4(1):1050. doi: 10.1038/s42003-021-02586-0.
10
Modulators of protein-protein interactions as antimicrobial agents.
RSC Chem Biol. 2021 Feb 3;2(2):387-409. doi: 10.1039/d0cb00205d. eCollection 2021 Apr 1.

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