{"url":"/dataset/molecule3d","name":"Molecule3D","full_name":null,"description_markdown":"Molecule3D is a new benchmark that includes a dataset with precise ground-state geometries of approximately 4 million molecules derived from density functional theory (DFT). It also provides a set of software tools for data processing, splitting, training, and evaluation, etc.","description_withheld":null,"homepage":"https://github.com/divelab/MoleculeX/tree/molx/Molecule3D","introduced_date":"2021-09-30","introduced_date_note":null,"introduced_by":{"paper":"/paper/molecule3d-a-benchmark-for-predicting-3d","title":"Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular Graphs","first_author":"Zhao Xu","url":null},"license":{"name":"Unknown","url":null},"modalities":[],"tasks":[{"name":"Molecular Property Prediction","url":"/task/molecular-property-prediction","datasets_with_task":"/datasets/task/molecular-property-prediction"},{"name":"3D Geometry Prediction","url":"/task/3d-geometry-prediction","datasets_with_task":"/datasets/task/3d-geometry-prediction"}],"languages":[],"variants":["Molecule3D","Molecule3D val","Molecule3D test"],"data_loaders":[],"num_papers_in_archive":17,"source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28"},"benchmarks":[{"leaderboard":"/sota/3d-geometry-prediction-on-molecule3d-test","task":"3D Geometry Prediction","dataset_variant":"Molecule3D test","rows":2,"metrics":["MAE","RMSE","Validity","Validity3D"],"first_row_in_archive_order":{"model":"DeeperGCN-DAGNN + Distance","paper":"/paper/molecule3d-a-benchmark-for-predicting-3d","metrics":{"MAE":"0.483","RMSE":"0.753","Validity":"1.69","Validity3D":"0.03"},"code_links":[{"title":"divelab/MoleculeX","url":"https://github.com/divelab/MoleculeX"},{"title":"chao1224/se3ddm","url":"https://github.com/chao1224/se3ddm"},{"title":"chao1224/geossl","url":"https://github.com/chao1224/geossl"}]},"note":"rows are the archive's own order at snapshot; nothing here re-ranks them"},{"leaderboard":"/sota/3d-geometry-prediction-on-molecule3d-val","task":"3D Geometry Prediction","dataset_variant":"Molecule3D val","rows":2,"metrics":["MAE","RMSE","Validity","Validity3D"],"first_row_in_archive_order":{"model":"DeeperGCN-DAGNN + Distance","paper":"/paper/molecule3d-a-benchmark-for-predicting-3d","metrics":{"MAE":"0.482","RMSE":"0.749","Validity":"1.71","Validity3D":"0.02"},"code_links":[{"title":"divelab/MoleculeX","url":"https://github.com/divelab/MoleculeX"},{"title":"chao1224/se3ddm","url":"https://github.com/chao1224/se3ddm"},{"title":"chao1224/geossl","url":"https://github.com/chao1224/geossl"}]},"note":"rows are the archive's own order at snapshot; nothing here re-ranks them"}],"papers_with_a_benchmark_row":[{"paper":"/paper/molecule3d-a-benchmark-for-predicting-3d","title":"Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular Graphs","date":"2021-09-30","rows_on_this_dataset":4,"code_links":3,"syntology":null}],"syntology_totals":{"read_at":"2026-09-24T18:15:14+00:00","papers_with_samples":0,"samples_harvested":0,"samples_ran":0,"samples_unverified":0,"pointer_only_for_licence":0,"papers_with_no_sample_that_ran":0,"note":"the per-paper counts above, summed; not a rate"},"papers_note":"The archive never published its papers-using-dataset list; these are papers with a leaderboard row on this dataset's benchmarks."}