Physics Aware Neural Networks for Unsupervised Binding Energy Prediction

Ke Liu, Hao Chen, Chunhua Shen
Proceedings of the 42nd International Conference on Machine Learning, PMLR 267:38169-38187, 2025.

Abstract

Developing models for protein-ligand interactions holds substantial significance for drug discovery. Supervised methods often failed due to the lack of labeled data for predicting the protein-ligand binding energy, like antibodies. Therefore, unsupervised approaches are urged to make full use of the unlabeled data. To tackle the problem, we propose an efficient, unsupervised protein-ligand binding energy prediction model via the conservation of energy (CEBind), which follows the physical laws. Specifically, given a protein-ligand complex, we randomly sample forces for each atom in the ligand. Then these forces are applied rigidly to the ligand to perturb its position, following the law of rigid body dynamics. Finally, CEBind predicts the energy of both the unperturbed complex and the perturbed complex. The energy gap between two complexes equals the work of the outer forces, following the law of conservation of energy. Extensive experiments are conducted on the unsupervised protein-ligand binding energy prediction benchmarks, comparing them with previous works. Empirical results and theoretic analysis demonstrate that CEBind is more efficient and outperforms previous unsupervised models on benchmarks.

Cite this Paper

BibTeX
@InProceedings{pmlr-v267-liu25f, title = {Physics Aware Neural Networks for Unsupervised Binding Energy Prediction}, author = {Liu, Ke and Chen, Hao and Shen, Chunhua}, booktitle = {Proceedings of the 42nd International Conference on Machine Learning}, pages = {38169--38187}, year = {2025}, editor = {Singh, Aarti and Fazel, Maryam and Hsu, Daniel and Lacoste-Julien, Simon and Berkenkamp, Felix and Maharaj, Tegan and Wagstaff, Kiri and Zhu, Jerry}, volume = {267}, series = {Proceedings of Machine Learning Research}, month = {13--19 Jul}, publisher = {PMLR}, pdf = {https://raw.githubusercontent.com/mlresearch/v267/main/assets/liu25f/liu25f.pdf}, url = {https://proceedings.mlr.press/v267/liu25f.html}, abstract = {Developing models for protein-ligand interactions holds substantial significance for drug discovery. Supervised methods often failed due to the lack of labeled data for predicting the protein-ligand binding energy, like antibodies. Therefore, unsupervised approaches are urged to make full use of the unlabeled data. To tackle the problem, we propose an efficient, unsupervised protein-ligand binding energy prediction model via the conservation of energy (CEBind), which follows the physical laws. Specifically, given a protein-ligand complex, we randomly sample forces for each atom in the ligand. Then these forces are applied rigidly to the ligand to perturb its position, following the law of rigid body dynamics. Finally, CEBind predicts the energy of both the unperturbed complex and the perturbed complex. The energy gap between two complexes equals the work of the outer forces, following the law of conservation of energy. Extensive experiments are conducted on the unsupervised protein-ligand binding energy prediction benchmarks, comparing them with previous works. Empirical results and theoretic analysis demonstrate that CEBind is more efficient and outperforms previous unsupervised models on benchmarks.} }
Endnote
%0 Conference Paper %T Physics Aware Neural Networks for Unsupervised Binding Energy Prediction %A Ke Liu %A Hao Chen %A Chunhua Shen %B Proceedings of the 42nd International Conference on Machine Learning %C Proceedings of Machine Learning Research %D 2025 %E Aarti Singh %E Maryam Fazel %E Daniel Hsu %E Simon Lacoste-Julien %E Felix Berkenkamp %E Tegan Maharaj %E Kiri Wagstaff %E Jerry Zhu %F pmlr-v267-liu25f %I PMLR %P 38169--38187 %U https://proceedings.mlr.press/v267/liu25f.html %V 267 %X Developing models for protein-ligand interactions holds substantial significance for drug discovery. Supervised methods often failed due to the lack of labeled data for predicting the protein-ligand binding energy, like antibodies. Therefore, unsupervised approaches are urged to make full use of the unlabeled data. To tackle the problem, we propose an efficient, unsupervised protein-ligand binding energy prediction model via the conservation of energy (CEBind), which follows the physical laws. Specifically, given a protein-ligand complex, we randomly sample forces for each atom in the ligand. Then these forces are applied rigidly to the ligand to perturb its position, following the law of rigid body dynamics. Finally, CEBind predicts the energy of both the unperturbed complex and the perturbed complex. The energy gap between two complexes equals the work of the outer forces, following the law of conservation of energy. Extensive experiments are conducted on the unsupervised protein-ligand binding energy prediction benchmarks, comparing them with previous works. Empirical results and theoretic analysis demonstrate that CEBind is more efficient and outperforms previous unsupervised models on benchmarks.
APA
Liu, K., Chen, H. & Shen, C.. (2025). Physics Aware Neural Networks for Unsupervised Binding Energy Prediction. Proceedings of the 42nd International Conference on Machine Learning, in Proceedings of Machine Learning Research 267:38169-38187 Available from https://proceedings.mlr.press/v267/liu25f.html.

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