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USearchMolecules: A Multi-Modal Atlas of 7 Billion Small Molecules

Authors: Vardanian, Ash;

USearchMolecules: A Multi-Modal Atlas of 7 Billion Small Molecules

Abstract

Large chem-informatics dataset of 7'131'914'291 small molecules with up to 50 heavy atoms, aggregated from PubChem, GDB13, and Enamine REAL, and enriched with machine-searchable representations of every molecule, growing over time. Those currently span 28 billion binary structural fingerprints computed with RDKit and CDK - MACCS with 166 dimensions, PubChem with 881, ECFP4 with 2048, and FCFP4 with 2048 - as well as 3D conformer geometries generated with ETKDG and optimized with MMFF94. Distributed as Parquet shards with pre-constructed USearch indexes for real-time similarity search and clustering across billions of molecules, hosted anonymously on the AWS Open Data platform, and accompanied by a bigger-than-memory Python pipeline with optional GPU acceleration for reproducing every stage.

If you use this dataset, please cite it as below.

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average