CANED: A PyMOL Plugin for Computer-Aided De Novo Enzyme Design

CANED is a PyMOL plugin designed to streamline de novo enzyme design by integrating advanced computational tools into a user-friendly interface. It provides menu bar navigation and click-based operations, with standardized file output formats. Combining Rosettas physical modeling and LigandMPNNs sequence prediction capabilities, CANED organizes the enzyme design workflow into three modular stages: File Preparation, Backbone Design, and Sequence Design. It supports preparation of multiple file formats, provides Rosettas matching methods to generate enzyme backbones, and offers diverse sequence design methods. Dynamic table-based analysis and real-time 3D visualization provide a more intuitive way to select high-quality design results. By reducing the need for computational expertise and command-line operations, CANED makes enzyme design accessible to a broader range of researchers, advancing applications in pharmaceuticals, biocatalysis, and sustainable chemistry.