An Online Server for Geometry-Aware Protein Function Annotations Through Predicted Structure.

Understanding protein functions is critical for metagenomic research, disease mechanism elucidation, and rational drug discovery. Traditional biochemical methods to determine protein functions are often inefficient and costly, leading to a widening gap between the rapid accumulation of protein sequences and their functional annotations. To address this, we introduce GPSFun, a fast and accurate web server that provides comprehensive geometry-aware protein sequence function annotations, including protein-binding sites for multiple ligands, gene ontologies, subcellular locations, and protein solubility. GPSFun's web server can be accessed at https://bio-web1.nscc-gz.cn/app/GPSFun , offering users a result with a rich visualized interface. Additionally, GPSFun was adopted to annotate ligand-binding sites for over 568,000 proteins from Swiss-Prot, leading to a complementary database named GPSiteDB ( https://bio-web1.nscc-gz.cn/database/GPSiteDB ). In this chapter, we first overview the workflow and results of our method, and then, we provide a step-by-step instruction on the usage of GPSFun and GPSiteDB, along with the detailed interpretations of the corresponding results.