Graph representation learning for structural proteomics

The field of structural proteomics, which is focused on studying the structure-function relationship of proteins and protein complexes, is experiencing rapid growth. Since the early 2000s, structural databases such as the Protein Data Bank are storing increasing amounts of protein structural data, in addition to modeled structures becoming increasingly available. This, combined with the recent advances in graph-based machine-learning models, enables the use of protein structural data in predictive models, with the goal of creating tools that will advance our understanding of protein function. Similar to using graph learning tools to molecular graphs, which currently undergo rapid development, there is also an increasing trend in using graph learning approaches on protein structures. In this short review paper, we survey studies that use graph learning techniques on proteins, and examine their successes and shortcomings, while also discussing future directions.