Molecular Databases & Datasets

Dataset cards covering large-scale molecular enumeration databases (GDB-11/13/17, ZINC-22) for virtual screening and drug discovery, and conformer ensemble datasets (GEOM, MARCEL) for molecular property prediction and 3D modeling.

Year	Dataset	Key Idea
2007	GDB-11: Chemical Universe Database (26.4M Molecules)	Systematic enumeration of 26.4M small organic molecules up to 11 heavy atoms
2009	GDB-13: Chemical Universe Database (970M Molecules)	Extension to 970M molecules up to 13 heavy atoms
2012	GDB-17: Chemical Universe Database (166.4B Molecules)	Largest enumeration database with 166.4B molecules up to 17 heavy atoms
2022	GEOM: Energy-Annotated Molecular Conformations Dataset	Energy-annotated molecular conformer ensembles for 3D modeling
2023	ZINC-22: A Multi-Billion Scale Database for Ligand Discovery	Over 37B make-on-demand molecules for virtual screening
2024	MARCEL: Molecular Conformer Ensemble Learning Benchmark	722K+ conformers across 76K+ molecules for conformer ensemble learning

Computational Chemistry

ZINC-22 Tranche Browser showing molecular count distribution

ZINC-22: A Multi-Billion Scale Database for Ligand Discovery

ZINC-22 is a multi-billion-scale public database containing over 37 billion make-on-demand molecules. It utilizes distributed infrastructure and specialized search algorithms to support modern ultra-large virtual screening campaigns.

Computational Chemistry

MARCEL dataset Kraken ligand example in 3D conformation

MARCEL: Molecular Conformer Ensemble Learning Benchmark

MARCEL provides a comprehensive benchmark for molecular representation learning with 722K+ conformers across four diverse subsets (Drugs-75K, Kraken, EE, BDE), enabling evaluation of conformer ensemble methods for property prediction in drug discovery and catalysis.

Computational Chemistry

GEOM dataset example molecule: N-(4-pyrimidin-2-yloxyphenyl)acetamide

GEOM: Energy-Annotated Molecular Conformations Dataset

GEOM contains 450k+ molecules with 37M+ conformations, featuring energy annotations from semi-empirical (GFN2-xTB) and DFT methods for property prediction and molecular generation research.

Computational Chemistry

GDB-11 molecule structure showing FC1C2OC1c3c(F)coc23

GDB-11: Chemical Universe Database (26.4M Molecules)

GDB-11 contains 26.4 million systematically generated small organic molecules with up to 11 atoms, establishing the methodology for exploring drug-like chemical space computationally.

Computational Chemistry

GDB-13 molecule structure showing CCCC(O)(CO)CC1CC1CN

GDB-13: Chemical Universe Database (970M Molecules)

GDB-13 contains nearly 1 billion systematically generated small organic molecules with up to 13 atoms, achieving billion-scale chemical space exploration while maintaining drug-like properties.

Computational Chemistry

GDB-17 molecule structure showing complex polycyclic architecture

GDB-17: Chemical Universe Database (166.4B Molecules)

GDB-17 contains 166.4 billion systematically generated small organic molecules with up to 17 atoms. It represents the most comprehensive exploration of drug-relevant chemical space achieved through computational enumeration.