AlphaPPIweb: an integration platform for protein-protein interaction prediction and evaluation

The advent of AlphaFold has markedly advanced structural biology by enabling highly accurate predictions of protein structures. This breakthrough has been further extended by AlphaFold-Multimer, which enables the prediction of protein complex structures. However, currently available tools for predictions have limitations, including usage constraints and the need for extensive postprediction analysis to identify interface residues. To address these challenges, we introduce AlphaPPIweb, a comprehensive web-based platform designed to leverage AlphaPulldown, an AlphaFold-Multimer-based tool, for predicting protein complex structures. Users simply input amino acid sequences, after which AlphaPPIweb generates three-dimensional structural predictions, provides confidence scores, and presents results through intuitive visualizations. The platform facilitates the prediction of interactions between a single bait protein and multiple candidate proteins, thus aiding in the identification of potential ligand-receptor interactions. Furthermore, AlphaPPIweb incorporates automated interface residue analysis immediately following structure prediction, streamlining the workflow and providing comprehensive insights into the predicted complexes. This integrated approach significantly enhances the usability of AlphaPPIweb for biomedical studies and educational applications. By democratizing access to advanced structural prediction tools and enabling a comprehensive analysis of protein interactions, AlphaPPIweb promotes extensive exploration and understanding within the biological research community. AlphaPPIweb is accessible at http://alphappiweb.cmu.edu.tw/.