2022
DOI: 10.1021/acsmedchemlett.1c00662
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Contemporary Computational Applications and Tools in Drug Discovery

Abstract: In the past decade or so there has been a dramatic increase in the number of computational applications and tools that have been developed to enable medicinal chemists to prosecute modern drug discovery programs more efficiently. The upsurge of user-friendly, well-designed computational tools that enable structure-based drug design (SBDD) and cheminformatics (CI)-based drug design has equipped the medicinal chemist with an arsenal of tools and applications that significantly augments the entire design process,… Show more

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Cited by 36 publications
(19 citation statements)
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“…Because our objective is to provide guidance to enzyme engineers, we emphasize the computational approaches aimed at manipulating the catalytic functions of existing enzymes, and, in general, excluded de novo design (reviewed elsewhere [16][17][18] ). We also do not review literature on the related problem of drug discovery, [19][20] although several of our raised points will apply in that field, too. We will discuss computational tools roughly in the order they occur in many sophisticated computational design workflows (Figure 2), although any given pipeline may diverge from this order, or skip some or even most other steps in this very general scheme.…”
Section: Introductionmentioning
confidence: 99%
“…Because our objective is to provide guidance to enzyme engineers, we emphasize the computational approaches aimed at manipulating the catalytic functions of existing enzymes, and, in general, excluded de novo design (reviewed elsewhere [16][17][18] ). We also do not review literature on the related problem of drug discovery, [19][20] although several of our raised points will apply in that field, too. We will discuss computational tools roughly in the order they occur in many sophisticated computational design workflows (Figure 2), although any given pipeline may diverge from this order, or skip some or even most other steps in this very general scheme.…”
Section: Introductionmentioning
confidence: 99%
“…Along with the acknowledgment of natural products research comes the challenge of identifying and quantifying the highly variable composition of natural extracts, selecting the lead compounds from a large number of promising compounds, as well as understanding their biochemical action and mechanism. The modern instrumental techniques for identifying and quantifying compounds, and the chemoinformatic, with its several experimental tools, have enabled medicinal chemists to achieve fast and effective drug discovery programs that have yielded promising results ( Cox and Gupta, 2022 ). The most remarkable example of the combined use of modern techniques was the research to identify the molecular mechanism of the SARS-CoV-2 virus and the search to develop new treatments for COVID-19 and its complications ( Mtewa et al, 2022 ).…”
Section: Introductionmentioning
confidence: 99%
“…Methods such as molecular structure property modeling have been used for decades in the pharmaceutical field in order to predict important properties, e.g., biological activity, solubility and toxicity, for prioritization of compounds with respect to potential toxicity issues and experimental testing [7]. For a recent review on computational tools, see reference [8]. The increasing focus on identifying undesirable toxic effects for chemical structures of interest, real or virtual, is manifested by recent publications such as [9,10] and recent reviews on machine learning (ML) techniques by Dara and co-workers [11] and by Matsuzaka and Yashiro [12].…”
Section: Introductionmentioning
confidence: 99%