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PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams
Journal of Computer-Aided Molecular Design ( IF 3.5 ) Pub Date : 2023-07-29 , DOI: 10.1007/s10822-023-00522-4
Konrad Diedrich 1 , Bennet Krause 1, 2 , Ole Berg 1 , Matthias Rarey 1
Affiliation  

In this article, we present PoseEdit, a new, interactive frontend of the popular pose visualization tool PoseView. PoseEdit automatically produces high-quality 2D diagrams of intermolecular interactions in 3D binding sites calculated from ligands in complex with protein, DNA, and RNA. The PoseView diagrams have been improved in several aspects, most notably in their interactivity. Thanks to the easy-to-use 2D editor of PoseEdit, the diagrams are extensively editable and extendible by the user, can be merged with other diagrams, and even be created from scratch. A large variety of graphical objects in the diagram can be moved, rotated, selected and highlighted, mirrored, removed, or even newly added. Furthermore, PoseEdit enables a synchronized 2D-3D view of macromolecule-ligand complexes simplifying the analysis of structural features and interactions. The representation of individual diagram objects regarding their visualized chemical properties, like stereochemistry, and general graphical styles, like the color of interactions, can additionally be edited. The primary objective of PoseEdit is to support scientists with an enhanced way to communicate ligand binding mode information through graphical 2D representations optimized with the scientist’s input in accordance with objective criteria and individual needs. PoseEdit is freely available on the ProteinsPlus web server (https://proteins.plus).



中文翻译:

PoseEdit:通过交互式 2D 图增强配体结合模式通信

在本文中,我们介绍 PoseEdit,这是流行姿势可视化工具 PoseView 的一个新的交互式前端。PoseEdit 自动生成 3D 结合位点中分子间相互作用的高质量 2D 图,该图是根据与蛋白质、DNA 和 RNA 复合的配体计算得出的。PoseView 图在多个方面进行了改进,最显着的是其交互性。得益于 PoseEdit 易于使用的 2D 编辑器,用户可以对图表进行广泛的编辑和扩展,可以与其他图表合并,甚至可以从头开始创建。图中的大量图形对象可以移动、旋转、选择和突出显示、镜像、删除甚至新添加。此外,PoseEdit 可实现大分子-配体复合物的同步 2D-3D 视图,从而简化结构特征和相互作用的分析。单个图表对象的可视化化学性质(如立体化学)和一般图形样式(如相互作用的颜色)的表示可以另外进行编辑。PoseEdit 的主要目标是为科学家提供一种增强的方式,通过根据客观标准和个人需求根据科学家的输入进行优化的图形 2D 表示来传达配体结合模式信息。PoseEdit 可在 Proteins Plus网络服务器 (https:// Proteins.plus) 上免费获取。

更新日期:2023-07-29
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