Predicting how a drug-like molecule binds to a specific protein target is a core problem in drug discovery. An extremely fast computational binding method would enable key applications such as fast virtual screening or drug engineering. Existing methods are computationally expensive as they rely on heavy candidate sampling coupled with scoring, ranking, and fine-tuning steps. We challenge this paradigm with EquiBind, an SE(3)-equivariant geometric deep learning model performing direct-shot prediction of both i) the receptor binding location (blind docking) and ii) the ligand’s bound pose and orientation. EquiBind achieves significant speed-ups and better quality compared to traditional and recent baselines. Further, we show extra improvements when coupling it with existing fine-tuning techniques at the cost of increased running time. Finally, we propose a novel and fast fine-tuning model that adjusts torsion angles of a ligand’s rotatable bonds based on closed form global minima of the von Mises angular distance to a given input atomic point cloud, avoiding previous expensive differential evolution strategies for energy minimization.

Prediction of a molecule’s 3D conformer ensemble from the molecular graph holds a key role in areas of cheminformatics and drug discovery. Existing generative models have several drawbacks including lack of modeling important molecular geometry elements (e.g., torsion angles), separate optimization stages prone to error accumulation, and the need for structure fine-tuning based on approximate classical force-fields or computationally expensive methods. We propose GEOMOL --- an end-to-end, non-autoregressive, and SE(3)-invariant machine learning approach to generate distributions of low-energy molecular 3D conformers. Leveraging the power of message passing neural networks (MPNNs) to capture local and global graph information, we predict local atomic 3D structures and torsion angles, avoid- ing unnecessary over-parameterization of the geometric degrees of freedom (e.g., one angle per non-terminal bond). Such local predictions suffice both for both the training loss computation and for the full deterministic conformer assembly (at test time). We devise a non-adversarial optimal transport based loss function to promote diverse conformer generation. GEOMOL predominantly outperforms popular open-source, commercial, or state-of-the-art machine learning (ML) models, while achieving significant speed-ups. We expect such differentiable 3D structure generators to significantly impact molecular modeling and related applications.