ArticleScientific data2022
GEOM, energy-annotated molecular conformations for property prediction and molecular generation.
Article in Scientific data, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 98 papers, 1 of them a synthesis that pooled it.
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Who cites it
98 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A systematic review of molecular representation learning foundation models.Briefings in bioinformatics · 2026Pooled it
- EXPECTATION-MAXIMIZATION FOR STRUCTURE DETERMINATION DIRECTLY FROM CRYO-EM MICROGRAPHS.Inverse problems and imaging (Springfield, Mo.) · 2027Article
- DesignMaster: a multi-conditional diffusion framework for rational PROTAC design.Bioinformatics (Oxford, England) · 2026Article
- Controllable molecular generation with fine-tuned flow-matching model.Communications chemistry · 2026Article
- ActivityDiff: a diffusion model with positive and negative activity guidance for de novo drug design.Bioinformatics (Oxford, England) · 2026Article
- Deep generative models for 3D structure-based drug design and molecular optimisation: a comprehensive survey.Journal of computer-aided molecular design · 2026Review
- FLOWR.ROOT - A flow matching-based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction.Nature communications · 2026Article
- Structure-aware artificial intelligence for next-generation drug discovery: from protein-ligand modeling to generative biomolecular design.Briefings in bioinformatics · 2026Review
- DrugDL: dual-modal deep learning framework for multi-property drug prediction and targeted therapy discovery.Bioinformatics (Oxford, England) · 2026Article
- Modular Framework for 3D Molecular Generation in Computational Chemistry Applications.Journal of the American Chemical Society · 2026Article
- Transforming Molecular Science With Large Language Models: From Molecule Understanding to Autonomous Scientific Discovery.Chemistry, an Asian journal · 2026Review
- DeepSnap: From Three-Dimensional Molecular Images to Quantitative Structure-Activity Predictions.International journal of molecular sciences · 2026Review
- Assessing the factors influencing the quality of pocket-conditioned 3D generative models.Journal of cheminformatics · 2026Article
- FlowMol3: flow matching for 3DDigital discovery · 2026Article
- Hypergraph learning with multi-dimensional metabolite feature extractions and static-dynamic attention mechanisms to fill missing reactions in metabolic networks.Briefings in bioinformatics · 2026Article
- Improving protein-ligand complex generation with force field guidance.Journal of cheminformatics · 2026Article
- A Comprehensive Dataset of Chemical Reactions Covering Second and Third Row Elements with Million-Scale Quantum Chemical Calculations.Scientific data · 2026Article
- NaviDiv: a web app for monitoring chemical diversity in generative molecular design.Digital discovery · 2026Article
- Generative Artificial Intelligence Transitions Pharmaceutical Development from Empirical Screening to Predictive Molecular Design and Clinical Trial Optimization.Pharmaceuticals (Basel, Switzerland) · 2026Review
- LaMGen: LLM-based 3D molecular generation for multi-target drug design.Nature communications · 2026Article
38 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.