# Quantum Neural Network applications to Protein Binding Affinity Predictions

arXiv: https://arxiv.org/abs/2508.03446 · HTML: https://mlsanity.com/paper/2508.03446/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 6 of its 43 references that are in the map.
- First posted on arXiv 5 Aug 2025.

## Builds on (most cited first, 6 of 6)

- [Variational Quantum Algorithms](https://mlsanity.com/paper/2012.09265/) (2020)
- [Quantum Data Encoding: A Comparative Analysis of Classical-to-Quantum Mapping Techniques and Their Impact on Machine Learning Accuracy](https://mlsanity.com/paper/2311.10375/) (2023)
- [A Survey on Quantum Machine Learning: Current Trends, Challenges, Opportunities, and the Road Ahead](https://mlsanity.com/paper/2310.10315/) (2023)
- [Quantum Computing: A Taxonomy, Systematic Review and Future Directions](https://mlsanity.com/paper/2010.15559/) (2020)
- [Near-Term Quantum Computing Techniques: Variational Quantum Algorithms, Error Mitigation, Circuit Compilation, Benchmarking and Classical Simulation](https://mlsanity.com/paper/2211.08737/) (2022)
- [A hybrid quantum-classical fusion neural network to improve protein-ligand binding affinity predictions for drug discovery](https://mlsanity.com/paper/2309.03919/) (2023)

## Abstract (arXiv)

Binding energy is a fundamental thermodynamic property that governs molecular interactions, playing a crucial role in fields such as healthcare and the natural sciences. It is particularly relevant in drug development, vaccine design, and other biomedical applications. Over the years, various methods have been developed to estimate protein binding energy, ranging from experimental techniques to computational approaches, with machine learning making significant contributions to this field. Although classical computing has demonstrated strong results in constructing predictive models, the variation of quantum computing for machine learning has emerged as a promising alternative. Quantum neural networks (QNNs) have gained traction as a research focus, raising the question of their potential advantages in predicting binding energies. To investigate this potential, this study explored the feasibility of QNNs for this task by proposing thirty variations of multilayer perceptron-based quantum neural networks. These variations span three distinct architectures, each incorporating ten different quantum circuits to configure their quantum layers. The performance of these quantum models was compared with that of a state-of-the-art classical multilayer perceptron-based artificial neural network, evaluating both accuracy and training time. A primary dataset was used for training, while two additional datasets containing entirely unseen samples were employed for testing. Results indicate that the quantum models achieved approximately 20% higher accuracy on one unseen dataset, although their accuracy was lower on the other datasets. Notably, quantum models exhibited training times several orders of magnitude shorter than their classical counterparts, highlighting their potential for efficient protein binding energy prediction.