Chemistry Datasets

Benchmark datasets for molecular property prediction, reactions, and more.

Benchmark Suites

Dataset	Description	Link
MoleculeNet	Comprehensive benchmark suite with multiple tasks	moleculenet.org
TDC	Therapeutics Data Commons — drug discovery datasets	tdcommons.ai
OCHEM	3.77M records for 689 chemical properties (CC BY 4.0)	ochem.eu

Molecular Structure Databases

Dataset	Description	Link
ZINC20	Chemical library for deep docking virtual screening	zinc20-ML
ZINC22	Commercially-available compounds for virtual screening	cartblanche22
COCONUT	Open-source natural products database	coconut
Crystallography Open Database	Open-access crystal structures	cod
GDB	Enumerated molecules following feasibility rules	gdb
Enamine HTS	1.93 million diverse screening compounds	enamine
GNPS	Mass spectrometry database for natural products	gnps
MoNA	Mass spectrometry database with real and predicted spectra	mona
nmrshiftdb2	Organic structures linked with NMR spectral data	nmrshiftdb2
nCov-Group Data	SMILES, fingerprints, descriptors for millions of compounds	ncov

Property Prediction Benchmarks

Dataset	Property	Link
AquaSolDB	Curated aqueous solubility data	harvard dataverse
BigSolDB 2.0	103,944 solubility values across solvents/temperatures	zenodo
ESol	Water solubility for organic small molecules	pubmed
FreeSolv	Experimental and calculated hydration free energies	github
Lipophilicity	Octanol/water distribution coefficients at pH 7.4	deepchem
Flashpoint	10,575 molecular flashpoint values	github
Harvard OPV	Photovoltaic data with quantum-chemical calculations	figshare
ILThermo	Ionic liquid thermodynamic and transport properties	nist
Photoswitch Dataset	405 curated photoswitch molecules	github
Leffingwell Odor	3,523 molecules with expert-labeled odor descriptors	zenodo
Limiting Activity Coefficients	Solvent/solute pair data	polybox

QM Datasets

Dataset	Description	Link
QM7/QM7b	Small organic molecules with properties	quantum-machine.org
QM8	Electronic spectra and excited state energies	quantum-machine.org
QM9	134K molecules with 13 properties from DFT	quantum-machine.org
MD Trajectories	Molecular dynamics simulation data	quantum-machine.org
SolProp	1 million COSMO-RS calculations and solvation data	mit
SOMAS	Solubility for redox-flow battery design	figshare

Bioactivity & Drug Discovery

Dataset	Description	Link
BindingDB	2.6M binding data entries for molecular recognition	bindingdb
ChEBI-20	33,010 molecule-description pairs for captioning	paperswithcode
Papyrus	Curated bioactivity combining ChEMBL and ExCAPE-DB	4tu
LIT-PCBA	15 target sets, 7761 actives, 382674 inactives	drugdesign
MPCD	39 datasets for activity prediction	github
MoleculeACE	Benchmark for activity cliff compounds	github
ACNet	400K Matched Molecular Pairs against 190 targets	acnet

Reaction Datasets

Dataset	Description	Link
USPTO	Reactions from US patents 1976-2016	figshare
Open Reaction Database	Standardized open reaction data	ord
RDB7	Atom-mapped SMILES with barrier heights and enthalpies	zenodo
Dreher-Doyle	3,955 Pd-catalyzed Buchwald-Hartwig reactions	github
Perera (Suzuki)	5,760 Pd-catalyzed Suzuki-Miyaura reactions	github

ADME & Pharmacology

Dataset	Description	Link
EPA CompTox	Chemistry, toxicity, exposure for 100K+ chemicals	epa
SIDER	Drug side effects (CC BY-NC-SA 4.0)	embl
Caco-2 Permeability	Drug absorption through intestinal tissue	figshare
PAMPA Permeability	Drug permeability assay data	doi
KEGG PATHWAY	Biological functions from molecular-level data	kegg
LOTUS	750,000+ structure-organism pairs	zenodo
MetXBioDB	Biotransformation reactions and metabolites	zenodo
ONSIDES	Adverse drug effects from FDA labels	github
HMDB	Small molecule metabolites in human body	hmdb
Guide to PHARMACOLOGY	Expert-curated ligand-activity-target (CC BY-SA 4.0)	iuphar
Clinical Trials	All study records from ClinicalTrials.gov	ct.gov
KD-DTI	Drug-target-interaction triplets	github
Metrabase	Human small molecule metabolism and transport	cam
Open Targets	Genetics/genomics for target identification	opentargets
Probes & Drugs	Bioactive compound libraries	probes-drugs
DDI Dataset	MedLine/DrugBank documents on drug interactions	paperswithcode

Text & NLP Datasets

Dataset	Description	Link
PubMed	Abstracts and citations from biomedical literature	pubmed
PubMed Central	Free full-text biomedical article archive	pmc
S2ORC	81.1M English academic papers (CC BY-NC 4.0)	github
ChemTables	788 chemical patent tables with labels (CC BY NC 3.0)	mendeley
NLMChem	150 manually annotated full-text articles on chemicals	nlm
PubChemSTM	281K chemical structure and text paired data	arxiv
Elsevier Corpus	40,001 open-access CC-BY articles	elsevier
Europe PMC	Bulk download of 5M+ full-text articles	europepmc
BioRxiv XML	Full-text bioRxiv via Amazon S3	biorxiv
MedRxiv XML	Medical research articles via S3	medrxiv
BC5CDR	1500 PubMed articles with annotated chemicals/diseases	paperswithcode
PubMedQA	QA dataset with 1K expert labels, 273.5K instances	pubmedqa

LLM Training Datasets

Dataset	Description	Size	Link
ChemPile	Mixture-of-expert chemical corpus	75B+ tokens	huggingface
SmolInstruct	Instruction dataset from 15 chemistry tasks	3.3M pairs	huggingface
CAMEL Chemistry	GPT-4 conversation pairs about chemistry	20K samples	huggingface
ChemNLP	Curated text for chemistry LLMs	80K records	huggingface
ChemLLMBench	Chemistry evaluation benchmark for LLMs	8 tasks	github
SciCode	Scientific coding reasoning benchmark	338 subproblems	github
ChemData 700K	Chemistry question-answer pairs	700K pairs	huggingface
MatSci-Instruct	Materials science instruction data	52K samples	huggingface
MoleculeQA	Molecular understanding benchmark	62K QA pairs	github
ChemBench	7-domain benchmarking across chemistry	2.7K questions	github
MatText	Benchmarking language representations of materials	-	github
MegaScience	Multi-domain science question answering	-	huggingface
ZINC20-ML	Deep-learning-ready ZINC20 formats	300M+	zinc20-ML

Literature-Mined Datasets

Dataset	Description	Size	Link
PubChem	Chemical information from 750+ data sources	116M compounds	pubchem
Open Reaction Database	Standardized chemical reaction data	1M+ reactions	ord
PatCID	Chemical structures from patent images	81M images	github
MatScholar	NLP-extracted materials entities	5M+ abstracts	matscholar
L2M3	Literature-mined materials-morphology database	51K entries	matscholar
ChemDataExtractor	Toolkit for auto-extracting chemical data	-	chemdataextractor

Reference Resources

Resource	Description	Link
IUPAC Gold Book	Chemistry terminology and definitions	iupac
LibreText Chemistry	Open-access chemistry textbook	libretexts
OpenStax Chemistry 2e	Free textbook (CC-BY 4.0)	openstax
ThermoML Archive	Thermophysical property data	nist

Dataset Collections

Resource	Description
awesome-matchem-datasets	Materials & chemistry datasets (Blaiszik)
awesome-chemistry-datasets	Curated list of ML-ready chemistry datasets
TDC	Therapeutics Data Commons — drug discovery datasets

Data Formats

Common formats you’ll encounter:

Format	Description	Tool
SMILES	String representation of molecules	RDKit
SDF/MOL	3D structure files	RDKit, OpenBabel
InChI	Unique molecular identifier	RDKit

Loading Data with RDKit


from rdkit import Chem
import pandas as pd
 
# From SMILES
mol = Chem.MolFromSmiles("CCO")
 
# From SDF file
suppl = Chem.SDMolSupplier("molecules.sdf")
mols = [mol for mol in suppl if mol is not None]
 
# From CSV with SMILES column
df = pd.read_csv("molecules.csv")
df["mol"] = df["smiles"].apply(Chem.MolFromSmiles)