# GEOM: Energy-annotated molecular conformations for property prediction and molecular generation

arXiv: https://arxiv.org/abs/2006.05531 · HTML: https://mlsanity.com/paper/2006.05531/

## Key facts

- Cited by 243 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 9 Jun 2020.

## Built on by (most cited first, 30 of 243)

- [Equivariant Diffusion for Molecule Generation in 3D](https://mlsanity.com/paper/2203.17003/) (2022)
- [GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation](https://mlsanity.com/paper/2203.02923/) (2022)
- [Torsional Diffusion for Molecular Conformer Generation](https://mlsanity.com/paper/2206.01729/) (2022)
- [Pre-training Molecular Graph Representation with 3D Geometry](https://mlsanity.com/paper/2110.07728/) (2021)
- [Spherical Message Passing for 3D Graph Networks](https://mlsanity.com/paper/2102.05013/) (2021)
- [Learning Gradient Fields for Molecular Conformation Generation](https://mlsanity.com/paper/2105.03902/) (2021)
- [Is Model Collapse Inevitable? Breaking the Curse of Recursion by Accumulating Real and Synthetic Data](https://mlsanity.com/paper/2404.01413/) (2024)
- [3D Infomax improves GNNs for Molecular Property Prediction](https://mlsanity.com/paper/2110.04126/) (2021)
- [Equivariant 3D-Conditional Diffusion Models for Molecular Linker Design](https://mlsanity.com/paper/2210.05274/) (2022)
- [GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles](https://mlsanity.com/paper/2106.07802/) (2021)
- [Diffusion-based Molecule Generation with Informative Prior Bridges](https://mlsanity.com/paper/2209.00865/) (2022)
- [MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation](https://mlsanity.com/paper/2302.09048/) (2023)
- [Learning Neural Generative Dynamics for Molecular Conformation Generation](https://mlsanity.com/paper/2102.10240/) (2021)
- [PINNacle: A Comprehensive Benchmark of Physics-Informed Neural Networks for Solving PDEs](https://mlsanity.com/paper/2306.08827/) (2023)
- [Adjoint Sampling: Highly Scalable Diffusion Samplers via Adjoint Matching](https://mlsanity.com/paper/2504.11713/) (2025)
- [Scientific Large Language Models: A Survey on Biological & Chemical Domains](https://mlsanity.com/paper/2401.14656/) (2024)
- [SE(3) Equivariant Graph Neural Networks with Complete Local Frames](https://mlsanity.com/paper/2110.14811/) (2021)
- [All-atom Diffusion Transformers: Unified generative modelling of molecules and materials](https://mlsanity.com/paper/2503.03965/) (2025)
- [Equivariant Energy-Guided SDE for Inverse Molecular Design](https://mlsanity.com/paper/2209.15408/) (2022)
- [Particle Guidance: non-I.I.D. Diverse Sampling with Diffusion Models](https://mlsanity.com/paper/2310.13102/) (2023)
- [ComENet: Towards Complete and Efficient Message Passing for 3D Molecular Graphs](https://mlsanity.com/paper/2206.08515/) (2022)
- [Molecular Geometry Pretraining with SE(3)-Invariant Denoising Distance Matching](https://mlsanity.com/paper/2206.13602/) (2022)
- [MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design](https://mlsanity.com/paper/2203.14500/) (2022)
- [MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation](https://mlsanity.com/paper/2305.07508/) (2023)
- [An End-to-End Framework for Molecular Conformation Generation via Bilevel Programming](https://mlsanity.com/paper/2105.07246/) (2021)
- [MDM: Molecular Diffusion Model for 3D Molecule Generation](https://mlsanity.com/paper/2209.05710/) (2022)
- [Geometrically Equivariant Graph Neural Networks: A Survey](https://mlsanity.com/paper/2202.07230/) (2022)
- [Swallowing the Bitter Pill: Simplified Scalable Conformer Generation](https://mlsanity.com/paper/2311.17932/) (2023)
- [Graph Generation with Diffusion Mixture](https://mlsanity.com/paper/2302.03596/) (2023)
- [Clifford Group Equivariant Neural Networks](https://mlsanity.com/paper/2305.11141/) (2023)

## Abstract (arXiv)

Machine learning (ML) outperforms traditional approaches in many molecular design tasks. ML models usually predict molecular properties from a 2D chemical graph or a single 3D structure, but neither of these representations accounts for the ensemble of 3D conformers that are accessible to a molecule. Property prediction could be improved by using conformer ensembles as input, but there is no large-scale dataset that contains graphs annotated with accurate conformers and experimental data. Here we use advanced sampling and semi-empirical density functional theory (DFT) to generate 37 million molecular conformations for over 450,000 molecules. The Geometric Ensemble Of Molecules (GEOM) dataset contains conformers for 133,000 species from QM9, and 317,000 species with experimental data related to biophysics, physiology, and physical chemistry. Ensembles of 1,511 species with BACE-1 inhibition data are also labeled with high-quality DFT free energies in an implicit water solvent, and 534 ensembles are further optimized with DFT. GEOM will assist in the development of models that predict properties from conformer ensembles, and generative models that sample 3D conformations.