Materials for Drug Development using AI

Drug dataset (Chem)

• ZINC15

https://zinc15.docking.org/

• ZINC20

https://zinc20.docking.org/

• MOSES (filtered ZINC)

https://github.com/molecularsets/moses

• ChEMBL

https://www.ebi.ac.uk/chembl/

• PubChem

https://pubchem.ncbi.nlm.nih.gov/

• DrugBank

https://go.drugbank.com/

• DUD-E

http://dude.docking.org/datasets

• ExCAPE-DB

https://solr.ideaconsult.net/search/excape/

• PHAROS

https://pharos.nih.gov/

• GDB

https://gdb.unibe.ch/downloads/

• QM

http://quantum-machine.org/datasets/

Benchmark dataset

• MoleculeNet

http://moleculenet.ai/

• GuacaMol

https://www.benevolent.com/guacamol

Genomics

• GEO

https://www.ncbi.nlm.nih.gov/geo/

• KEGG

https://www.genome.jp/kegg/

• OMIM

https://www.omim.org/

• PheGenI

https://www.ncbi.nlm.nih.gov/gap/phegeni

• HGNC

https://www.genenames.org/

• gnomAD

https://gnomad.broadinstitute.org/

• ArrayExpress

https://www.ebi.ac.uk/arrayexpress/

• Cytotoxicity Database

https://ctdbase.org/

• GDAC

https://gdac.broadinstitute.org/

Cancer Genomics

• DepMap

https://depmap.org/portal/

• TCGA

https://portal.gdc.cancer.gov/

http://firebrowse.org/ (for data downloading)

• ICGC

https://icgc.org/

• cBioPortal

https://www.cbioportal.org/

• COSMIC

https://cancer.sanger.ac.uk/census

• Cancer Hallmarks Genes

http://bio-bigdata.hrbmu.edu.cn/CHG/index.html

• NCI-60

https://dtp.cancer.gov/discovery_development/nci-60/

• NCI TPW

https://tpwb.nci.nih.gov/GeneExpressionNCI60/TPWorkbench/

• CTRP

https://portals.broadinstitute.org/ctrp/

• GDSC

https://www.cancerrxgene.org/

• Cancer Therapeutics Response Portal

https://www.broadinstitute.org/ctrp

• CellMiner

https://discover.nci.nih.gov/cellminer/home.do

• CellMinerCDB

https://discover.nci.nih.gov/rsconnect/cellminercdb/

Drug-induced Gene Expression Profiles

• LINCS

http://lincsportal.ccs.miami.edu/dcic-portal/

Single Cell Genomics

• 10x Genomics

https://support.10xgenomics.com/single-cell-gene-expression/datasets/

Pharmacogenomics

• PharmGKB

https://www.pharmgkb.org/

• PharmVar

https://www.pharmvar.org/

• NCI DREAM

http://dreamchallenges.org/project/dream-7-nci-dream-drug-sensitivity-prediction-challenge/

• PharmacoDB

https://pharmacodb.ca/

Human Interactome

• STRING

https://string-db.org/

• PINA

https://omics.bjcancer.org/pina/

• HuRI

http://www.interactome-atlas.org/

• ClueGO

http://apps.cytoscape.org/apps/cluego

• Cytoscape

https://cytoscape.org/

• BIOGRID

https://thebiogrid.org/

• Interactome

https://ccsb.dana-farber.org/interactome-data.html

Cancer Cell Line Encyclopedia

• CCLE

https://portals.broadinstitute.org/ccle

GO Analysis

• DAVID

https://david.ncifcrf.gov/

Gene Set Enrichment Analysis

• GSEA

https://www.gsea-msigdb.org/gsea/index.jsp

• Enrichr

https://maayanlab.cloud/Enrichr/

Protein Database

• Uniprot

https://www.uniprot.org/

• Pfam

https://pfam.xfam.org/

Protein Structure

• PDB

https://www.rcsb.org/

• SWISS-MODEL

https://swissmodel.expasy.org/

Chemical-Protein interaction

• STITCH

http://stitch.embl.de/

Software

• Schrodinger

https://www.schrodinger.com/

• Rosetta

https://www.rosettacommons.org/software

• Spark

https://www.cresset-group.com/software/spark/

Side Effect

• SIDER 4.1

http://sideeffects.embl.de/

• OFFSIDES

http://tatonettilab.org/offsides/

Medical Terminology

• MedDRA

https://www.meddra.org/

ADMET

• admetSAR

http://lmmd.ecust.edu.cn/admetsar2/

EHR

• MIMIC

https://mimic.mit.edu/docs/gettingstarted/

freely-available medical research data

• PhysioNet

https://physionet.org/about/database/

Frequently used database in clinical practice

• UpToDate

https://www.uptodate.com/contents/search

• IBM Micromedex

https://www.micromedexsolutions.com/home/dispatch

Molecular Dynamics

• GROMACS

https://www.gromacs.org/

• AmberTools

https://ambermd.org/AmberTools.php

• NAMD

https://www.ks.uiuc.edu/Research/namd/

• Martini (force-field)

http://cgmartini.nl/

Related good paper

• A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspective

https://arxiv.org/abs/2102.10062

To be updated...