TANKBind: Trigonometry-Aware Neural NetworKs for Drug-Protein Binding Structure Prediction

Wei Lu, Qifeng Wu, Jixian Zhang, Jiahua Rao, Chengtao Li, Shuangjia Zheng

Keywords: drug-protein interaction, protein-ligand docking, molecular docking, drug discovery, proteins, molecules, geometry deep learning, trigonometry, deep learning, neural networks

TL;DR: We introduce a trigonometry-aware neural network to efficiently predict physically-allowed inter-molecular interaction between protein and small molecule.

Abstract: Illuminating interactions between proteins and small drug molecules is a long-standing challenge in the field of drug discovery. Despite the importance of understanding these interactions, most previous works are limited by hand-designed scoring functions and insufficient conformation sampling. The recently-proposed graph neural network-based methods provides alternatives to predict protein-ligand complex conformation in a one-shot manner. However, these methods neglect the geometric constraints of the complex structure and weaken the role of local functional regions. As a result, they might produce unreasonable conformations for challenging targets and generalize poorly to novel proteins. In this paper, we propose Trigonometry-Aware Neural networKs for binding structure prediction, TANKBind, that builds trigonometry constraint as a vigorous inductive bias into the model and explicitly attends to all possible binding sites for each protein by segmenting the whole protein into functional blocks. We construct novel contrastive losses with local region negative sampling to jointly optimize the binding interaction and affinity. Extensive experiments show substantial performance gains in comparison to state-of-the-art physics-based and deep learning-based methods on commonly-used benchmark datasets for both binding structure and affinity predictions with variant settings.