BiSim Tool: a binding simulation tool to aid and simplify ligand-binding assay design and development.

IF 16.4 1区化学 Q1 CHEMISTRY, MULTIDISCIPLINARY

Accounts of Chemical Research Pub Date : 2024-04-17 DOI:10.4155/bio-2023-0242

Lien Dejager, Sophia Banton, Patricia Marques, Gabriela Rinikova, Sabrina Lory, Elizabeth S Hickford, Carole Martin-Hamka, Mark Penney, Sasker Grootjans

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引用次数: 0

Abstract

Ligand-binding assays (LBAs) rely on the reversible, noncovalent binding between the analyte of interest and the assay reagents, and understanding their dynamic equilibrium is key to building robust LBA methods. Although the dynamic interplay of free and bound fractions can be calculated using mathematical models, these are not routinely applied. This approach is costly in terms of both assay development time and reagents, and can result in an under-exploration of the possible parameter combinations. Therefore, we have created a user-friendly simulation tool to facilitate LBA development (the BiSim Tool). We describe the models driving the mathematical simulations and the main features of our software solution by means of case studies, illustrating the tool's value in drug development. To support drug development for all patients worldwide, the BiSim Tool is now available as an open-source code project and as a free web-based tool at https://proteinbindingsimulation.shinyapps.io/BiSim-ProteinBindingSimulation [1].

查看原文本刊更多论文

BiSim 工具：用于辅助和简化配体结合检测设计和开发的结合模拟工具。

配体结合检测（LBAs）依赖于相关分析物与检测试剂之间可逆的非共价结合，了解它们的动态平衡是建立稳健的 LBA 方法的关键。虽然游离部分和结合部分的动态相互作用可以通过数学模型计算出来，但这些模型并没有得到常规应用。这种方法耗费了大量的检测开发时间和试剂，而且可能导致对可能的参数组合探索不足。因此，我们创建了一个用户友好型模拟工具（BiSim 工具），以促进 LBA 的开发。我们将通过案例研究介绍驱动数学模拟的模型以及我们软件解决方案的主要功能，从而说明该工具在药物开发中的价值。为了支持全球所有患者的药物开发，BiSim 工具现已作为一个开放源代码项目和免费网络工具在 https://proteinbindingsimulation.shinyapps.io/BiSim-ProteinBindingSimulation [1]上提供。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Accounts of Chemical Research 化学-化学综合

CiteScore

31.40

自引率

1.10%

发文量

312

审稿时长

2 months

期刊介绍： Accounts of Chemical Research presents short, concise and critical articles offering easy-to-read overviews of basic research and applications in all areas of chemistry and biochemistry. These short reviews focus on research from the author’s own laboratory and are designed to teach the reader about a research project. In addition, Accounts of Chemical Research publishes commentaries that give an informed opinion on a current research problem. Special Issues online are devoted to a single topic of unusual activity and significance. Accounts of Chemical Research replaces the traditional article abstract with an article "Conspectus." These entries synopsize the research affording the reader a closer look at the content and significance of an article. Through this provision of a more detailed description of the article contents, the Conspectus enhances the article's discoverability by search engines and the exposure for the research.