ProteinCT: An implementation of the protein circuit topology framework

Duane Moes, Elnaz Banijamali, Vahid Sheikhhassani, Barbara Scalvini, Jaie Woodard, Alireza Mashaghi

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)


The ability to describe the topology of a folded protein conformation is critically important for functional analysis, protein engineering, and drug design. Circuit topology is a unique topological framework which is widely applicable to protein analysis, yet a state-of-the art implementation of this concept is lacking. Here, we present an open-source Python-implemented circuit topology tool called ProteinCT. The platform provides a method for acquiring, visualizing, analyzing, and quantifying circuit topology data from proteins of interest. We mapped the universe of human proteins to a circuit topology space using conventional hardware within a few hours, demonstrating the performance of ProteinCT. In brief,
• A Python-implemented circuit topology tool is developed to extract global and local topological information from a protein structure file.
• Modules are developed to combine topological information with geometric and energetic information.
• It is demonstrated that the method can be efficiently applied to a large set of proteins, opening a wide range of possibilities for structural proteomics research.
Original languageEnglish
Article number101861
Number of pages8
Publication statusPublished - 2022


  • Structural biology
  • Topology
  • Circuit topology
  • Protein
  • Contact


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