ProtGlycanDock: Towards Accurate Protein-Glycan Docking with Tailored Dataset, Benchmark and Model

Minghao Xu, Jiaze Song, Jinyu Wang, Wentao Zhang

Performing accurate protein-glycan docking is critical to understanding protein-glycan interactions which govern many biological processes. However, this important task is hampered by the lack of tailored datasets, benchmarks and models for protein-glycan docking. To fill this blank, we first curate a standard benchmark ProtGlycanDock for training and evaluating protein-glycan docking models under both protein and glycan generalization settings. On this benchmark, we evaluate ten models in three categories, physics-based docking methods, machine-learning-based docking models and molecular structure prediction models. To obtain more precise binding poses, we further propose two finetuning techniques to inject the knowledge of glycan conformations into a general-purpose molecular structure prediction model. These two techniques respectively augment model inputs with glycan topological features and refine glycan binding pose with a glycan energy loss. Benchmark results show the superiority of AlphaFold 3 among existing methods, and the two proposed finetuning techniques can be well combined to achieve a state-of-the-art model for protein-glycan docking. Also, we perform stratified…