PoseEdit

PoseEdit automatically generates editable 2D diagrams of intermolecular interactions in 3D binding sites from ligands in complex with protein, DNA, and RNA to support communication of ligand binding mode information.

Key Features:

• Automatic 2D Diagram Generation: Produces high-quality 2D diagrams of intermolecular interactions in protein-ligand, DNA-ligand, and RNA-ligand complexes.
• Interaction Estimation: Estimates interactions between molecules using an underlying interaction model that relies on atom types and simple geometric criteria.
• Extensive Diagram Editing: Allows translation, rotation, mirroring, selection, highlighting, removal, and addition of graphical objects and interactions in the 2D diagram.
• Customizable Labels and Styles: Enables addition of individual labels, adjustment of available labels, and editing of visualized chemical properties such as stereochemistry and graphical styles including interaction colors.
• Diagram Merging and Creation: Supports merging diagrams with other diagrams and creating diagrams from scratch.
• Synchronized 2D-3D View: Provides a synchronized 2D-3D view of macromolecule-ligand complexes to simplify analysis of structural features and interactions.
• Multiple Export Formats: Supports download of final 2D diagrams in JSON or SVG format.

Scientific Applications:

• Binding Site Analysis: Facilitates analysis of structural features and interactions in macromolecule-ligand complexes through synchronized 2D-3D visualization.
• Ligand Binding Mode Communication: Supports scientists in communicating ligand binding mode information through graphical 2D representations optimized with scientific input.
• Structure Mining Integration: Utilizes the same interaction model as the structure mining tool GeoMine to describe binding sites.

Methodology:

Interactions between molecules are estimated by an underlying interaction model that relies on atom types and simple geometric criteria.