BACKGROUND: The volume of protein sequence data has grown exponentially in recent years, driven by advancements in metagenomics. Despite this, a substantial proportion of these sequences remain poorly annotated, underscoring the need for robust bioinformatics tools to facilitate efficient characterisation and annotation for functional studies. RESULTS: We present PyPropel, a Python-based computational tool developed to streamline the large-scale analysis of protein data, with a particular focus on applications in machine learning. PyPropel integrates sequence and structural data pre-processing, feature generation, and post-processing for model performance evaluation and visualisation, offering a comprehensive solution for handling complex protein datasets. CONCLUSION: PyPropel provides added value over existing tools by offering a unified workflow that encompasses the full spectrum of protein research, from raw data pre-processing to functional annotation and model performance analysis, thereby supporting efficient protein function studies.