ClusterONE Web: a tool for discovering and analyzing overlapping protein complexes

Abstract

Protein–protein interactions (PPIs) are central to many cellular processes, and the assembly of proteins into complexes is essential for biological function. Clustering with overlapping neighborhood expansion (ClusterONE) has been successfully used to detect overlapping protein complexes in both weighted and unweighted PPI networks. Here, we present ClusterONE Web, a freely available, web-based tool that brings the functionality of ClusterONE into an accessible, user-friendly environment. The platform includes a database of preprocessed PPI datasets covering multiple organisms, reducing the need for manual data collection and preprocessing, while also allowing users to upload their own interaction data. Detected complexes are presented through an interactive interface, facilitating their exploration without requiring specialized software installation. The server also provides built-in Gene Ontology enrichment analysis to aid in the functional interpretation of identified complexes. ClusterONE Web is platform-independent and available at https://paccanarolab.org/clusteroneweb/.