ProteinCT: An implementation of the protein circuit topology framework
Duane Moes,
Elnaz Banijamali,
Vahid Sheikhhassani,
Barbara Scalvini,
Jaie Woodard,
Alireza Mashaghi
Affiliations
Duane Moes
Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden 2333 CC, the Netherlands
Elnaz Banijamali
Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden 2333 CC, the Netherlands; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
Vahid Sheikhhassani
Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden 2333 CC, the Netherlands
Barbara Scalvini
Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden 2333 CC, the Netherlands
Jaie Woodard
Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden 2333 CC, the Netherlands
Alireza Mashaghi
Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden 2333 CC, the Netherlands; Corresponding author.
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.
