ProteinCT: An implementation of the protein circuit topology framework.
MethodsX 2022;
9:101861. [PMID:
36187158 PMCID:
PMC9520010 DOI:
10.1016/j.mex.2022.101861]
[Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/11/2022] [Indexed: 11/22/2022] Open
Abstract
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.
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