# HBGSA: Hydrogen Bond Graph with Self-Attention for Drug-Target Binding Affinity Prediction

arXiv: https://arxiv.org/abs/2604.23115 · HTML: https://mlsanity.com/paper/2604.23115/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 9 of its 37 references that are in the map.
- First posted on arXiv 25 Apr 2026.

## Builds on (most cited first, 9 of 9)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [DeepDTA: Deep Drug-Target Binding Affinity Prediction](https://mlsanity.com/paper/1801.10193/) (2018)
- [Structure-aware Interactive Graph Neural Networks for the Prediction of Protein-Ligand Binding Affinity](https://mlsanity.com/paper/2107.10670/) (2021)
- [Development and evaluation of a deep learning model for protein-ligand binding affinity prediction](https://mlsanity.com/paper/1712.07042/) (2017)
- [WideDTA: prediction of drug-target binding affinity](https://mlsanity.com/paper/1902.04166/) (2019)
- [Multi-task Bioassay Pre-training for Protein-ligand Binding Affinity Prediction](https://mlsanity.com/paper/2306.04886/) (2023)
- [HAC-Net: A Hybrid Attention-Based Convolutional Neural Network for Highly Accurate Protein-Ligand Binding Affinity Prediction](https://mlsanity.com/paper/2212.12440/) (2022)

## Built on by (most cited first, 1 of 1)

- [Blending experimental electron density information to protein-ligand interaction](https://mlsanity.com/paper/2610.14862/) (2026)

## Abstract (arXiv)

Accurate prediction of drug-target binding affinity accelerates drug discovery by prioritizing compounds for experimental validation. Current methods face three limitations: sequence-based approaches discard spatial geometric constraints, structure-based methods fail to exploit hydrogen bond features, and conventional loss functions neglect prediction-target correlation, a key factor for identifying high-affinity compounds in virtual screening. We developed HBGSA (Hydrogen Bond Graph with Self-Attention), a 3.06M-parameter model that encodes hydrogen bond spatial features. HBGSA uses graph neural networks to model hydrogen bond spatial topology with self-attention enhancement and Pearson correlation loss. Experimental results on PDBbind Core Set and CSAR-HiQ dataset demonstrate that HBGSA outperforms baseline methods with strong generalization capability. Ablation studies confirm the effectiveness of hydrogen bond modeling and Pearson correlation loss.