Protein-ligand binding prediction is a fundamental problem in AI-driven drug discovery. Previous work focused on supervised learning methods for small molecules where binding affinity data is abundant, but it is hard to apply the same strategy to other ligand classes like antibodies where labelled data is limited. In this paper, we explore unsupervised approaches and reformulate binding energy prediction as a generative modeling task. Specifically, we train an energy-based model on a set of unlabelled protein-ligand complexes using SE(3) denoising score matching (DSM) and interpret its log-likelihood as binding affinity. Our key contribution is a new equivariant rotation prediction network for SE(3) DSM called Neural Euler's Rotation Equations (NERE). It predicts a rotation by modeling the force and torque between protein and ligand atoms, where the force is defined as the gradient of an energy function with respect to atom coordinates. Using two protein-ligand and antibody-antigen binding affinity prediction benchmarks, we show that NERE outperforms all unsupervised baselines (physics-based potentials and protein language models) in both cases and surpasses supervised baselines in the antibody case.

Protein-ligand binding prediction is a fundamental problem in AI-driven drug discovery.

Protein-ligand binding prediction is a fundamental problem in AI-driven drug discovery. Previous work focused on supervised learning methods for small molecules where binding affinity data is abundant, but it is hard to apply the same strategy to other ligand classes like antibodies where labelled data is limited. In this paper, we explore unsupervised approaches and reformulate binding energy prediction as a generative modeling task. Specifically, we train an energy-based model on a set of unlabelled protein-ligand complexes using SE(3) denoising score matching (DSM) and interpret its log-likelihood as binding affinity. Our key contribution is a new equivariant rotation prediction network called Neural Euler's Rotation Equations (NERE) for SE(3) DSM. It predicts a rotation by modeling the force and torque between protein and ligand atoms, where the force is defined as the gradient of an energy function with respect to atom coordinates. Using two protein-ligand and antibody-antigen binding affinity prediction benchmarks, we show that NERE outperforms all unsupervised baselines (physics-based potentials and protein language models) in both cases and surpasses supervised baselines in the antibody case.

Protein-ligand binding prediction is a fundamental problem in AI-driven drug discovery. Previous work focused on supervised learning methods for small molecules where binding affinity data is abundant, but it is hard to apply the same strategy to other ligand classes like antibodies where labelled data is limited. In this paper, we explore unsupervised approaches and reformulate binding energy prediction as a generative modeling task. Specifically, we train an energy-based model on a set of unlabelled protein-ligand complexes using SE(3) denoising score matching (DSM) and interpret its log-likelihood as binding affinity. Our key contribution is a new equivariant rotation prediction network called Neural Euler's Rotation Equations (NERE) for SE(3) DSM.

Protein-ligand binding prediction is a fundamental problem in AI-driven drug discovery. Prior work focused on supervised learning methods using a large set of binding affinity data for small molecules, but it is hard to apply the same strategy to other drug classes like antibodies as labelled data is limited. In this paper, we explore unsupervised approaches and reformulate binding energy prediction as a generative modeling task. Specifically, we train an energy-based model on a set of unlabelled protein-ligand complexes using SE(3) denoising score matching and interpret its log-likelihood as binding affinity. Our key contribution is a new equivariant rotation prediction network called Neural Euler's Rotation Equations (NERE) for SE(3) score matching. It predicts a rotation by modeling the force and torque between protein and ligand atoms, where the force is defined as the gradient of an energy function with respect to atom coordinates. We evaluate NERE on protein-ligand and antibody-antigen binding affinity prediction benchmarks. Our model outperforms all unsupervised baselines (physics-based and statistical potentials) and matches supervised learning methods in the antibody case.