PoseEdit:通过交互式二维图增强配体结合模式通信

IF 3 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY
Konrad Diedrich, Bennet Krause, Ole Berg, Matthias Rarey
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引用次数: 2

摘要

在这篇文章中,我们介绍了PoseEdit,一个流行的姿势可视化工具PoseView的新的交互式前端。PoseEdit自动生成高质量的2D分子间相互作用图,从蛋白质、DNA和RNA的复合物的配体中计算出3D结合位点。PoseView图在几个方面得到了改进,最显著的是它们的交互性。由于PoseEdit易于使用的2D编辑器,这些图可以被用户广泛地编辑和扩展,可以与其他图合并,甚至可以从头创建。可以移动、旋转、选择和突出显示关系图中的各种图形对象、镜像、删除,甚至添加新对象。此外,PoseEdit支持大分子配体复合物的同步2D-3D视图,简化了结构特征和相互作用的分析。单独的图表对象的表示,关于它们的可视化化学性质,如立体化学,和一般的图形样式,如交互的颜色,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来交流配体结合模式信息,通过图形化的二维表示,根据客观标准和个人需求优化科学家的输入。PoseEdit在ProteinsPlus web服务器(https://proteins.plus)上免费提供。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams

PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams

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).

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来源期刊
Journal of Computer-Aided Molecular Design
Journal of Computer-Aided Molecular Design 生物-计算机:跨学科应用
CiteScore
8.00
自引率
8.60%
发文量
56
审稿时长
3 months
期刊介绍: The Journal of Computer-Aided Molecular Design provides a form for disseminating information on both the theory and the application of computer-based methods in the analysis and design of molecules. The scope of the journal encompasses papers which report new and original research and applications in the following areas: - theoretical chemistry; - computational chemistry; - computer and molecular graphics; - molecular modeling; - protein engineering; - drug design; - expert systems; - general structure-property relationships; - molecular dynamics; - chemical database development and usage.
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