Physics Aware Neural Networks for Unsupervised Binding Energy Prediction

Ke Liu, Hao Chen, Chunhua Shen

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.

Lay Summary:

(1) Protein-ligand binding affinity prediction is significant for drug discovery. (2) We propose an unsupervised protein-ligand binding energy prediction method. (3) This will advance the field of Machine
Learning and Computational Biology.

Application-Driven Machine Learning: This submission is on Application-Driven Machine Learning.

Primary Area: Applications->Everything Else

Keywords: Protein-ligand binding

Submission Number: 757