juProt: A web application for comparative analysis of protein-ligand interactomes

Comparative analysis of protein-ligand interactomes is crucial for understanding binding specificity, drug efficacy, and the impact of structural changes such as mutations. However, comparing the full spectrum of non-covalent interactions between different complexes often requires manual data extraction and complex workflows. We developed juProt, an open-source web application, to automate and streamline the comparative analysis of the complete protein-ligand interactome. juProt is developed in Julia using the Genie.jl framework and integrates the Protein-Ligand Interaction Profiler (PLIP) for comprehensive interaction detection. Users can either upload local PDB structures or automatically fetch files directly from the RCSB PDB using PDB IDs. The application detects and compares the full range of non-covalent interactions, including Hydrogen Bonds, Hydrophobic Contacts, π-Stacking, Salt Bridges, and Water Bridges. It generates comparative outputs including quantitative metrics, fold-change calculations, and 2D spatial pocket projections to visually map the geometric distribution of interacting residues. Validation against standalone PLIP using 20 diverse protein-ligand complexes (experimental and docked) demonstrated 100% concordance across all supported interaction types. A case study on human aromatase and its inhibitors (Letrozole, Anastrozole) interacting with native and mutant forms showcased juProt's utility. The analysis revealed that the Met364Thr mutation significantly remodeled the hydrophobic core of the Letrozole binding site, a structural insight clearly illustrated by the comparative 2D spatial mapping. juProt offers a robust, user-friendly methodology for the comparative analysis of the complete protein-ligand interactome. By automating data retrieval, calculating quantitative fold-changes, and generating spatially explicit 2D pocket projections, it significantly lowers the barrier for comprehensive structural analysis without requiring specialized graphics software. The tool is freely available at juprot.info.

The online version contains supplementary material available at 10.1007/s40203-026-00588-6.