Datasets for Drug Discovery and Development

Interaction Dataset

Drug-Target Interaction (DTI)

Dataset Name	Link	Description (Optional)
DAVIS	link
KIBA	link
BindingDB	link
BIOSNAP
DrugTargetCommons
KEGG
BRENDA
SuperTarget
GPCRdb
STITCH
TTD
PDBBind

Disease-Gene Interaction (DGI)

Dataset Name	Link	Description (Optional)
BIOSNAP
DisGeNET

Protein-Protein Interaction (PPI)

Dataset Name	Link	Description (Optional)
BIOSNAP
HuRI
STRING
Biocreative PPI

Drug-Drug Interaction (DDI)

Dataset Name	Link	Description (Optional)
DrugBank
DeepDDI
BIOSNAP
Twosides

Drug Property Dataset

High-Throughput Screening Assay (HTS)

Dataset Name	Link	Description (Optional)
SARS-CoV2-3CLPro-AID1706

Quantitative Structure–Activity Relationship (QSAR)

Dataset Name	Link	Description (Optional)
QsarDB	link

Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET)

Dataset Name	Link	Description (Optional)
ESOL
Lipophilicity
SIDER
OFFSIDES
HIA		absorption. Binary label. 499 positive samples and 78 negative samples.
bioavailability-eDrug3D		absorption. Binary label. 492 positive samples and 150 negative samples.
bioavailability		absorption. percentage, continuous label, 529 samples.
CACO-2		absorption. continuous label, 1,272 samples.
BBB		Distribution. Binary label. 1,282 positive samples and 310 negative samples.
PPBR		Distribution. Binary label. 411 positive samples and 356 negative samples.
CYP2C19		metabolism. Binary label. "1" means xxx, "0" means. 5,905 positive samples and 7,522 negative samples.
CYP2D6		metabolism. Binary label. "1" means xxx, "0" means. 2,769 positive samples and 11,127 negative samples.
CYP3A4		metabolism. Binary label. "1" means xxx, "0" means. 2,769 positive samples and 11,127 negative samples.
half-life-eDrug3D		excretion. continuous label. 1,250 samples.
Clearance-eDrug3D		excretion. continuous label. 963 samples.
Tox21	link	Toxicity. 7,832 samples.
ToxCast	link	Toxicity. 8,598 samples. Binary label.
ClinTox	link	Toxicity. 1,485 samples. Binary label.

Quantum Mechanics (QM)

Dataset Name	Link	Description (Optional)
QM7
QM8
QM9

Protein Functions Dataset

Protein Structural Classification (SRTUCT)

Dataset Name	Link	Description (Optional)
SCOP
dSPP
CATH

Protein Quality Assessment (QA)

Dataset Name	Link	Description (Optional)
Rosetta-300K
CASP13

Drugs Dataset

Drug Molecular Graphs/SMILES (Drug2D)

Dataset Name	Link	Description (Optional)
ZINC
ChEMBL
PubChem

Drug Molecular Graphs/SMILES (Drug3D)

Dataset Name	Link	Description (Optional)
e-Drug3D	link

Repurposing Library (REPURPOSE)

Dataset Name	Link	Description (Optional)
Broad Repurposing Hub

Proteins Dataset

Protein Amino Acid Sequence (Protein1D)

Dataset Name	Link	Description (Optional)
UniProt
NDB

Protein Amino Acid Sequence (Protein3D)

Dataset Name	Link	Description (Optional)
PDB

Biomedical Knowledge Graph

Dataset Name	Link	Description (Optional)
HetioNet
ogbn-biokg
DRKG

Chemical Synthesis Dataset

Retrosynthesis (RetroSyn)

Dataset Name	Link	Description (Optional)
USPTO-50K

Reaction Yields Prediction (YIELDS)

Dataset Name	Link	Description (Optional)
Buchwald-Hartwig
Suzuki-Miyaura

Pharmacogenomics Dataset

Pharmacogenomics Knowledge Base (KB)

Dataset Name	Link	Description (Optional)
PharmGKB

Drug Response Prediction (DrugResponse)

Dataset Name	Link	Description (Optional)
CCLE
GDSC

Drug Synergy Prediction (DrugSyn)

Dataset Name	Link	Description (Optional)
NCI-DREAM
OncoPolyPharmacology
NCI-ALMANAC

Clinical Trial Dataset

Dataset Name	Link	Description (Optional)
ATTC
ICTRP

microRNA Dataset

Dataset Name	Link	Description (Optional)
HMDD

Chemical Reaction Dataset

Dataset Name	Link	Description (Optional)
USPTO-50k