Chemical Information Sources/SIRCh/Chemistry Databases on the Web Classified

SIRCh: Selected Internet Resources for Chemistry

CLASSIFIED LIST

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ALPHABETICAL LIST

General (All Types of Compounds)
PubChem about PubChem ChemDB, the UC Irvine ChemDB (about ChemDB)
 * PubChemSR (Search and Retrieve) Tool (Developed by Junguk Hur: Download zip file from the Tools section; for Windows only). (about PubChemSR)
 * Wikipedia's entry on PubChem

ZINC (commercially-available compounds for virtual screening) (about ZINC)

Chemical Structure Lookup Service (CSLS): a database locator service (about CSLS)


 * CSLS Mirror site

ChemIDplus (US National Library of Medicine) (about ChemIDplus)

ChemFinder (CambridgeSoft; requires plugin for substructure searching) (about ChemFinder)

Chemspace (about Chemspace)

ChemSpider (ChemZoo) (about ChemSpider)

eMolecules (formerly Chmoogle) (about eMolecules)

Fisher Scientific (about Fisher)

ChemExper Chemical Dictionary (about ChemExper)

Query Chem (about Query Chem)

Generated Database of Chemical Universe of Small Molecules (about Generated DB)

Patent Analysis Free Databases (about Patent Analysis Free DB)

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2D Structure Searchable Databases
Chemical Structure Lookup Service (CSLS): a database locator service (about CSLS)


 * CSLS Mirror site

ChemIDplus (US National Library of Medicine) (about ChemIDplus)

ChemFinder (CambridgeSoft; requires plugin for substructure searching) (about ChemFinder)

Organic Syntheses (Requires plugin for substructure searching) (about Organic Syntheses)

eMolecules (formerly Chmoogle) (about eMolecules)

WebReactions (about WebReactions)

Fisher Scientific (about Fisher)

Calculation of Molecular Properties and Drug-Likeness (Molinspiration) (about Calculation)

Substructure Search of SRC's Pointer File (Syracuse Research Corporation) (about SRC's Pointer File)

ChemExper Chemical Dictionary (about ChemExper)

Query Chem (about Query Chem)

PubChem (use the Sketch option on this page) (about PubChem)

KEGG Ligand Database (about KEGG)

BindingDB; The Binding Database (University of Maryland Biotechnology Institute) (about BindingDB)

Sigma-Aldrich Chemistry Database (about Sigma-Aldrich)

ChemMine (Center for Plant Cell Biology, UC Riverside) (about ChemMine)

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Reaction Databases
Organic Syntheses (Requires plugin for substructure searching) (about Organic Syntheses)

WebReactions (about WebReactions)

Synthesis Protocols (Boston University Center for Chemical Methodology and Library Development) (about Synthesis Protocols)

ChemSynthesis Chemical Database

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Specific Classes of Compounds
Glycan Database (about Glycan DB)

Organic Syntheses (Requires plugin for substructure searching) (about Organic Syntheses)

LipidBank (about LipidBank)

LIPIDAT (thermodynamic and associated information on lipid mesophase and crystal polymorphic transitions) (about LIPIDAT)

HIC-Up, Hetero-compound Information Centre, Uppsala (about HIC-Up)

BRENDA, The Comprehensive Enzyme Information System (about BRENDA)

CAZy, Carbohydrate-Active enZymes (about CAZy)

Metlin Metabolite Database (about Metlin)

Metalloprotein Database and Browser (about Metalloprotein DB)

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Drug-Related Databases
PubDock; Docking PubChem for Discovery (Indiana University) (about PubDock)

ChemBank (about ChemBank)

US National Cancer Institute Developmental Therapeutics Program (about US NCI DTP)


 * Investigational Drugs – Chemical Information
 * DTP Data Search
 * COMPARE Database and Analysis tools for cancer research

Collaborative Drug Discovery Database (about CDD DB)

Calculation of Molecular Properties and Drug-Likeness (Molinspiration) (about Calculation)

Pharmabase: a database of cellular physiology & pharmacology (about Pharmabase)

Biopharmaceutical Products in the U.S. and European Markets (about Biopharmaceutical Products)

ChemMine (Center for Plant Cell Biology, UC Riverside) (about ChemMine)

National Drug Code Directory (US) (FDA Center for Drug Evaluation and Research) (about National DCD)

DrugBank (University of Alberta) (about DrugBank)

MEDPHYT (The Medicinal Plants Database) (about MEDPHYT)

Cytochrome P450 Drug Interaction table (Indiana University – Purdue University – Indianapolis) (about Cytochrome P450 DI table)

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Disease-Related Databases
HIV/OI/TB Therapeutics Database (US NIAID Division of AIDS) (about Therapeutics DB)

Therapeutic Target Database (about Therapeutic Target DB)

US National Cancer Institute Developmental Therapeutics Program (about US NCI DTP)

NIH DTP Cancer Cell Line Activity Predictions (Indiana University) (about NIH DTP Cancer Cell Line DB)

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Physical Properties, Spectra, etc.
NIST Chemistry WebBook (US National Institute for Standards and Technology) (about NIST Chemistry WebBook)

Atomic Reference Data for Electronic Structure Calculations (US National Institute for Standards and Technology) (about Atomic Reference Data)

NDRL/NIST Solution Kinetics Database on the Web (US National Institute for Standards and Technology) (about NDRL/NIST Solution Kinetics DB)

IUPAC-NIST Solubility Database (Data compiled and evaluated by the International Union of Pure and Applied Chemistry) (about IUPAC-NIST Solubility DB)

The Physical Properties Database (PHYSPROP) (Syracuse Research Corporation) (about PHYSPROP)

BindingDB; The Binding Database (University of Maryland Biotechnology Institute) (about Binding DB)

SOLV-DB (Solvents data from the National Center for Manufacturing Sciences) (about SOLV-DB)

Infotherm Thermophysical Properties Database (FIZ Chemie Berlin) (about Infortherm Thermophysical Properties DB)

Joint Expert Speciation System, JESS (Tool for tool for thermodynamic and kinetic modeling of chemical speciation in complex aqueous environments) (about JESS)

PDSP Ki Database (about PDSP K DB)

Bordwell pKa Table (Activity in DMSO) (University of Wisconsin) (about Bordwell pKa Table)

Chemical Kinetics Database on the Web (data on gas phase reactions from the US National Institute for Standards and Technology) (about Chemical Kinetics DB)

ChemxSeer (Penn State University) (chemical kinetics) (about ChemxSeer)

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Material Safety Data Sheets (MSDS)
MatWeb, a searchable database of material data sheets (about MatWeb)

CCOHS Web Information Service (about CCOHS)

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Spectral and Separations Databases
Spectral Database for Organic Compounds, SDBS (National Institute of Advanced Industrial Science and Technology (AIST), Japan) (about SDBS)

NMRShift DB (about NMRShift DB)

glycoSCIENCES.DE (about glycoSCIENCES.DE)

SUGABASE, carbohydrate NMR database (about SUGABASE)

Biological Magnetic Resonance Data Bank, BioMagResBank, BMRB (about BioMagResBank)

SPECARB, Raman spectra of carbohydates (about SPECARB)

EUROSPEC, International Spectroscopic Database (about EUROSPEC)

Chirbase, a molecular database for chiral chromatography (about Chirbase)

I-ChemiSt – Mass spec and NMR databases (about I-ChemiSt)

Proton NMR Spectra of Xyloglucans (about Proton NMR Spectra of Xyloglucans)

GC-EIMS of Partially Methylated Alditol Acetates (about GC-EIMS)

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Crystallography Databases
American Mineralogist Crystal Structure Database (about American Mineralogist CS DB)

Biological Macromolecule Crystallization Database (about Biological Macromolecule Cryst DB)

Indiana University Molecular Structure Center (about IU MSC)

Crystallography Open Database, COD (about COD)

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Toxicity and Environmental Databases
National Toxicology Program (US Department of Health and Human Services) (about NTP)

Envirofacts Master Chemical Integrator (EMCI) (US EPA) (about Envirofacts)

TOXNET, Toxicology Data Network (US National Library of Medicine) (about TOXNET)

CAMEO Chemicals (US National Oceanographic and Atmospheric Administration) (about CAMEO)

EXTOXNET, the Extension Toxicology Network (about EXTOXNET)

ECOTOX (US Environmental Protection Agency) (about ECOTOX)

Dr. Duke's Phytochemical and Ethnobotanical Databases (about Dr. Duke's)

Environmental Fate Database (Syracuse Research Corporation) (about Environmental Fate DB)

CCOHS Web Information Service (about CCOHS)

SOLV-DB (Solvents data from the National Center for Manufacturing Sciences) (about SOLV-DB)

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Biomolecule Databases
Entrez, the Life Science Search Engine (US National Center for Biotechnology Information) (about Entrez)

BRENDA, The Comprehensive Enzyme Information System (about BRENDA)

CAZy, Carbohydrate-Active enZymes (about CAZy)

NetPhosK 1.0 Server (about NetPhosK)

KEGG Ligand Database (about KEGG Ligand DB)

BioMeta Database (CMBI) (about BioMeta DB)

ChEBI, Chemical Entities of Biological Interest (EMBL-EBI, European Bioinformatics Institute) (about ChEBI)

CEBS, Chemical Effects in Biological Systems (NIEHS, National Institute of Environmental Health Sciences) (about CEBS)

Glycan Database (about Glycan DB)

PDB, Protein Data Bank (about PDB)

OWL, Composite Protein Sequence Database (Covers SWISS-PROT, PIR, GenBank, and NRL-3D) (about OWL)

UniProt (about UniProt)

SCOP, Structural Classification of Proteins (about SCOP)

CATH, Protein Structure Classification (about CATH)

iHOP, information Hyperlinked Over Proteins (about iHOP)

Nucleic Acids Database (Rutgers University: a repository of three-dimensional structural information about nucleic acids) (about Nucleic Acids DB)

DisProt – Database of Protein Disorder (about DisProt)

Human Protein Reference Database (about Human Protein Ref DB)

Flexweb; Analysis of Flexibility in Biomolecules and Networks (about Flexweb)

Proteins Database at National Chemical Laboratory (Pune, India) (about Proteins DB)

Human Metabolome Database (about Human Metabolome DB)

Metlin Metabolite Database (about Metlin)

IntAct (Protein Interaction Database) (about IntAct)

DIP Database of Interacting Proteins (about DIP)

BOND Biomolecular Object Network Database (about BOND)

SitesBase (about SitesBase)

BioGRID (about BioGRID)

NAViGaTOR (about NAViGaTOR)

MINT Molecular Interactions Database (about MINT)

Binding MOAD (University of Michigan) (about Binding MOAD)

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Metabolic Pathways
BiGG (virtual human metabolic network) (about BiGG)

MetaCyc Encyclopedia of Metabolic Pathways (about MetaCyc Encycylopedia)

KEGG Pathway (about KEGG Pathway)

Biochemical Pathways Database Under C@ROL (BioPath) (University of Erlangen) (about Biochemical Pathways DB)

LIPID MAPS (Lipid Metabolites And Pathways Strategy) (about LIPID MAPS)

Pathway Interaction Database (about Pathway Interaction DB)

Reactome, a curated knowledgebase of biological pathways (about Reactome)

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Web Services-enabled Bioscience Databases
myGRID (about myGRID)

bioMOBY (about bioMOBY)

TeraGrid Bioportal (about TeraGrid Bioportal)

Life Science Gateway (about Life Science Gateway)

GADU VO at Open Science Grid (about GADU VO)

KEGG API (about KEGG API)

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Journals
PubMed Central (PMC) (about PubMed)

PubMed Central (UK) (about PubMed Central (UK))

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Selected Commercial Databases
Chemical Abstracts Service (about CAS DBs)

AurSTORE Databases (Aureus Sciences) (about AurSTORE)

BioPrint (Cerep) (about BioPrint)

DrugMatrix (Iconix Pharmaceuticals) (about DrugMatrix)

ChemBioBase Suite (Jubilant Biosystems) (about ChemBioBase)

Kinase Knowledgebase (KKB) (Eidogen-Sertanty) (about KKB)

Biopath.Explore (about Biopath.Explore)

KiNET Proteomics Database (about KiNET Proteomics DB)

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Miscellaneous Databases
Medical Subject Headings, MeSH (US National Library of Medicine) (about MeSH)

Chemical Acronyms Database (maintained by the Indiana University Chemistry Library) (about Chemical Acronyms DB)

Glossary of Common Terms and Abbreviations in Quantum Chemistry (Karl K. Irikura) (about Glossary)

QCLDB II – Quantum Chemistry Literature DataBase (about QCLDB II)

CCCBDB Computational Chemistry Comparison and Benchmark Database (US National Institute for Standards and Technology) (about CCCBDB)

MedChem/Biobyte QSAR Database (Pomona College) (about QSAR DB)

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Finding Other Chemistry Databases
Sung Kwang's Cheminformation Homepage

Biophysical Chemistry Databases (University of Wisconsin) (about Biophysical Chemistry DBs)

NIST Data Gateway (about NIST Data Gateway)

NIST Scientific and Technical Databases (US National Institute for Standards and Technology) (about NIST S&T DBs)

NIST Physics Laboratory Physical Reference Data (US National Institute for Standards and Technology) (about NIST Physics Lab Phys Ref Data)

Data & Property Calculation Web Sites (University of Illinois, Chicago Thermodynamics Research Laboratory) (about Property Calc Web Sites)

NIOSH Databases and Information Resources (US National Institute for Occupational Safety and Health) (about NIOSH DBs)

For other chemistry databases, including commercial sources, see the Chemical Information/Databases section at For bioinformatics databases, see the
 * Links for Chemists (University of Liverpool)
 * the Compounds, Molecules section of Chemdex (University of Sheffield), and the
 * Cheminformatics Links and Data Sets sections of Cheminformatics.org.
 * OBRC; Online Bioinformatics Resources Collections] or the

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