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首页> 外文期刊>IEEE/ACM transactions on computational biology and bioinformatics >nAPOLI: A Graph-Based Strategy to Detect and Visualize Conserved Protein-Ligand Interactions in Large-Scale
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nAPOLI: A Graph-Based Strategy to Detect and Visualize Conserved Protein-Ligand Interactions in Large-Scale

机译：Napoli：基于图的策略，用于检测和可视化大规模的保守蛋白质 - 配体相互作用的策略

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摘要

Essential roles in biological systems depend on protein-ligand recognition, which is mostly driven by specific non-covalent interactions. Consequently, investigating these interactions contributes to understanding how molecular recognition occurs. Nowadays, a large-scale data set of protein-ligand complexes is available in the Protein Data Bank, what led several tools to be proposed as an effort to elucidate protein-ligand interactions. Nonetheless, there is not an all-in-one tool that couples large-scale statistical, visual, and interactive analysis of conserved protein-ligand interactions. Therefore, we propose nAPOLI (Analysis of PrOtein-Ligand Interactions), a web server that combines large-scale analysis of conserved interactions in protein-ligand complexes at the atomic-level, interactive visual representations, and comprehensive reports of the interacting residues/atoms to detect and explore conserved non-covalent interactions. We demonstrate the potential of nAPOLI in detecting important conserved interacting residues through four case studies: two involving a human cyclin-dependent kinase 2 (CDK2), one related to ricin, and other to the human nuclear receptor subfamily 3 (hNR3). nAPOLI proved to be suitable to identify conserved interactions according to literature, as well as highlight additional interactions. Finally, we illustrate, with a virtual screening ligand selection, how nAPOLI can be widely applied in structural biology and drug design. nAPOLI is freely available at bioinfo.dcc.ufmg.brapoli/.
机译：生物系统中的必要作用取决于蛋白质 - 配体识别，其主要由特定的非共价相互作用驱动。因此，调查这些相互作用有助于了解分子识别如何发生。如今，蛋白质数据库中可获得大规模的蛋白质 - 配体复合物，其中达到几种工具作为阐明蛋白质 - 配体相互作用的努力。尽管如此，没有一体化工具，耦合大规模的统计，视觉和互动分析的保守蛋白质 - 配体相互作用。因此，我们提出了Napoli（蛋白质 - 配体相互作用的分析），该网站服务器将蛋白质 - 配体复合物中的保守相互作用的大规模分析在原子水平，交互式视觉陈述和互动残留物/原子的综合报告中结合了大规模分析检测和探索保守的非共价相互作用。我们证明了Napoli通过四个案例研究检测重要的保守相互作用残留物的潜力：两种涉及人对依赖性激酶2（CDK2），与蓖麻素相关的一种，以及人核受体亚家族3（HNR3）。 Napoli被证明是适合根据文献识别保守的相互作用，并突出额外的相互作用。最后，通过虚拟筛选配体选择，Napoli如何广泛应用于结构生物学和药物设计。 Napoli在BioInfo.dcc.ufmg.brapoli/中自由提供。

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