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

• Published in: Journal of computer-aided molecular design Vol. 37; no. 10; pp. 491 - 503
• Main Authors: Diedrich, Konrad, Krause, Bennet, Berg, Ole, Rarey, Matthias
• Format: Journal Article
• Language: English
• Published: Cham Springer International Publishing 01.10.2023; Springer Nature B.V
• Subjects: Animal Anatomy; Binding sites; Chemical properties; Chemistry; Chemistry and Materials Science; Computer Applications in Chemistry; Graphical representations; Histology; Ligands; Morphology; Physical Chemistry; Proteins; Scientists; Stereochemistry; PoseView; Protein–ligand complexes; Molecular interactions; Pose diagrams; Mutable molecule visualization; Protein Data Bank; 2D structure diagrams
• ISSN: 0920-654X; 1573-4951; 1573-4951
• DOI: 10.1007/s10822-023-00522-4

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 Proteins Plus web server ( https://proteins.plus ).