Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada.
Department of Computer Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
Nucleic Acids Res. 2023 Jan 6;51(D1):D509-D516. doi: 10.1093/nar/gkac939.
Recent advances in Cryo-EM led to a surge of ribosome structures deposited over the past years, including structures from different species, conformational states, or bound with different ligands. Yet, multiple conflicts of nomenclature make the identification and comparison of structures and ortholog components challenging. We present RiboXYZ (available at https://ribosome.xyz), a database that provides organized access to ribosome structures, with several tools for visualisation and study. The database is up-to-date with the Protein Data Bank (PDB) but provides a standardized nomenclature that allows for searching and comparing ribosomal components (proteins, RNA, ligands) across all the available structures. In addition to structured and simplified access to the data, the application has several specialized visualization tools, including the identification and prediction of ligand binding sites, and 3D superimposition of ribosomal components. Overall, RiboXYZ provides a useful toolkit that complements the PDB database, by implementing the current conventions and providing a set of auxiliary tools that have been developed explicitly for analyzing ribosome structures. This toolkit can be easily accessed by both experts and non-experts in structural biology so that they can search, visualize and compare structures, with various potential applications in molecular biology, evolution, and biochemistry.
近年来，冷冻电镜技术的进步使得核糖体结构的研究取得了突飞猛进的发展，包括来自不同物种、构象状态或与不同配体结合的结构。然而，命名法的多重冲突使得结构和同源组件的识别和比较具有挑战性。我们介绍了 RiboXYZ（可在 https://ribosome.xyz 上获得），这是一个数据库，提供了对核糖体结构的有组织访问，具有几个用于可视化和研究的工具。该数据库与蛋白质数据库（PDB）保持同步，但提供了标准化的命名法，允许在所有可用结构中搜索和比较核糖体组件（蛋白质、RNA、配体）。除了对数据进行结构化和简化访问外，该应用程序还具有几个专门的可视化工具，包括配体结合位点的识别和预测，以及核糖体组件的 3D 叠加。总的来说，RiboXYZ 提供了一个有用的工具包，通过实现当前的约定并提供一组专门为分析核糖体结构开发的辅助工具，补充了 PDB 数据库。这个工具包可以很容易地被结构生物学领域的专家和非专家访问，以便他们可以搜索、可视化和比较结构，在分子生物学、进化和生物化学等方面具有各种潜在的应用。
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