Protein contact network explorer: topological analysis of protein structures

Abstract

Introduction The functions of proteins are primarily governed by coordinated interactions among amino acid residues throughout their three-dimensional structures. Large-scale determination of protein structures has long been made possible by experimental and computational methods; however, studying complex, dynamic, or multimeric systems remains challenging. Protein contact networks (PCNs) offer a graph-based representation of residue-level interactions and enable the application of network analysis techniques to structural data. Nevertheless, many existing tools mainly focus on creating static networks, which limits analytical flexibility. Methods In this study, we introduce Protein Contact Network Explorer (PCNE), a tool for simple construction, visualisation, and analysis of protein contact networks derived from structure data. Results The tool provides flexible residue contact definitions, the exploration of interactive networks, and the extraction of graph-theoretic measures relevant to understanding protein stability, allosteric communication, and functional organisation. Discussion PCNE supports the analysis of key interaction patterns, facilitating both exploratory and hypothesis-driven research in structural biology. The PCNE can be accessed via https://lactdr5rfibhg9m5tmamwg.streamlit.app/.