PyMOL plugin for Protein Circuit Topology

Circuit Topology (CT) is a fundamental property of folded polymer chains and provides a unique and powerful topological framework for protein analysis, with applications in functional annotation, disease marker identification, protein engineering, and drug development. An open-source Python-based implementation of CT, called ProteinCT, provides access to circuit topology analysis through a scripting environment. Here, we present the ProteinCT tool as a plugin for the molecular visualization platform PyMOL, packaged with a graphical user interface (GUI), easy automatic installation, and novel features developed through strong integration with PyMOL’s application programming interface (API). In addition to ProteinCT tools, the plugin includes CT tools for studying the dynamics of disordered proteins. Analysis of a representative protein trajectory confirms that the original functionality of ProteinCT is retained, the GUI is functional, easy to use, and visually clear, and the additional features are seamlessly integrated with PyMOL, making protein circuit topology widely accessible to researchers in structural biology and related fields.