Sorry, this page is currently in an outdated state, we are aware that some of the information is outdated or links might be broken.

The following table is a compilation of web sites we've found that offer chemical structural databases (of small molecules), with at least one of the following capabilities:

  • Search by (sub-) structure
  • Display of the structure, at least in 2D (not just a name)
  • Download/save a structure in a computer-readable format (SD, PDB...)
  • Retrieve/dump large parts of the database (or even the entire DB) in bulk form, again in a computer-readable format
  • Perform some kind of calculation on the structure (e.g. physicochemical properties etc.)
  • At least 100 molecules available
  • Accessible with just a web browser, possibly with some easily obtainable plugin (this excludes services that require a special application)

We found the following lists of links to contain useful URLs of chemistry search services, and in fact used them to help compile our table.
http://geocities.com/soaringbear/biomed/chem.html
http://www.liv.ac.uk/Chemistry/Links/refdatabases.html
http://chemfinder.cambridgesoft.com/siteslist.asp

The table is roughly sorted according to the order: government sites; academic sites; commercial sites. We know that this list is incomplete; and we're quite certain that it contains errors and inaccuracies. We therefore welcome any feedback with corrections and additions. Please e-mail Marc Nicklaus.

Name of DB Purpose
(main)
Organization URL Number of molecules Formula search SS search Name
search
SMILES search CAS-RN search Upload search
file
Registration
necessary
Fees 2D
display
3D
display
Save/export structure Bulk
downl.
Ext.
links
Plugins
needed
Problems encountered
NCI Web-
Accessible Data
Provide access, for searching and downloading, to public NCI structures and screening data DTP/NCI http://dtp.nci.nih.gov/
(select: Data Search; or: Discovery -> Web-Accessible Data and Tools)
250,000 - yes yes - (by NSC #) - - - yes yes yes yes yes Chime -
Enhanced NCI Database Browser Release 2 Search, visualize, export, link from, bulk-download structures, assay data and calculated properties of the Open NCI Database CCC, Germany
&
LMC/NCI
German mirror:
http://131.188.127.153/services/ncidb2/
U.S. mirror:
/ncidb2/
250,000 yes yes yes yes yes yes (only for background searches, necessary for hit sets of more than 10,000 compounds) - yes yes yes yes yes Chime optional; VRML plugin optional (please let us know if you find some :-)  )
Computational
 Chemistry
 Comparison
 and Benchmark
 DataBase (CCCBDB)
View QM results NIST http://srdata.nist.gov/cccbdb/ 613 yes - - - - - - - yes - (yes -
QM input,
output files)
- yes
(to NIST
WebBook)
- -
WebBook View spectra NIST http://webbook.nist.gov/ ~40,000 yes yes yes - yes yes - - yes - yes - - - -
Anti-HIV/OI Find cpds. tested against HIV NIAID http://chemdb.niaid.nih.gov/ 40,000 yes - yes - yes - - - yes - - - yes - -
ChemIDplus Locate structures and chem. inf. in NLM's databases SIS/NLM http://chem.sis.nlm.nih.gov/chemidplus/ 108,000 yes yes yes - yes - - - some some - - (to other NLM  DBs) Chime 3D display didn't work
NTP TRs Search the NTP Toxicology Reports NIEHS http://ntp-db.niehs.nih.gov/Main_Pages/
pub-Structures.html
500 - - yes - - - - - yes yes yes - - Chime or RasMol name search didn't work; browsing list OK
NTP Website Search the NTP test results, status and reports NIEHS http://ntp-server.niehs.nih.gov/cgi/iH_Indexes/
ALL_SRCH/iH_ALL_SRCH_Frames.html
?
(>200)
- - yes - yes - - - in some documents in some documents yes - ? Chime or RasMol -
HazDat Retrieve release and effects data of hazardous   substances Agency for Toxic Substances and Disease Registry http://www.atsdr.cdc.gov/hazdat.html 152 - - yes - - - - - yes yes yes - yes RasMol -
SOLV-DB View structures, properties of solvents NMCS http://solvdb.ncms.org/solvdb.htm ~180 yes - yes - yes - - - yes - - - - - some structure drawings didn't display
MSC Retrieve info. on small molecule crystals studied at IUMSC Indiana University Molecular Structure Center http://www.iumsc.indiana.edu/db/search.jsp >2,400 yes - yes - - - - - - yes yes - - (Java 1.2.1 optional) -
Common Compound Library View structures, properties and other info on substances encountered in introductory chem. courses Frostburg State University http://antoine.frostburg.edu/chem/senese/101/
compounds/library.shtml
800 yes - yes - - - - - yes - - - yes Chime -
Klotho View, retrieve biochemical compounds and stereochemical representations Wshington Univ. St.. Louis http://www.ibc.wustl.edu/klotho/ 439 - - (index) - - - - - yes yes yes - RasMol -
Hazardous Chemical Database View info. for hazardous chemicals Univ. of Akron, J. K. Hardy http://ull.chemistry.uakron.edu/erd/ 3,100 (as key- word) - yes - (as key- word) - - - yes - - - - - -
LipiDat View, retrieve structures and data of lipids Ohio State Univ. http://www.lipidat.chemistry.ohio-state.edu/
search.stm

       ([1] using specific lipid nomenclature)

20,000 (yes [1]) yes (yes [1]) - - yes (only for search structure upload) - yes ??? ??? - - Chime registration, display didn't work
Molecular Models View, retrieve calculated 3D structures Okanagan Univ. College, D. Woodcock http://www.ouc.bc.ca/chem/molecule/molecule.html 1,400 yes - yes - - - - - yes yes yes - - Chime, RasMol -
Chemicals with Pharma- ceutical Activity View, retrieve common pharmaceuticals Oxford Univ., UK http://www.chem.ox.ac.uk/mom/chemical-database/ 400 - - (index) - - - - - yes yes yes - - Chime and others -
SDBS View spectral data National Institute of Advanced Industrial Science and Technology, Japan http://www.aist.go.jp/RIODB/SDBS/menu-e.html 30,000 yes - yes - yes - - - yes - - - - - -
Relibase View
Protein
Ligands

CCDC
http://relibase.ccdc.cam.ac.uk
http://relibase.rutgers.edu
http://relibase.ebi.ac.uk
3,500 unique ligands
(12,000 proteins;
44,000 binding sites)
- yes yes yes - - - - yes yes (only PDB file) - yes (PDB) Relibase,
RasMol
or
RasWin
-
Lolas-WWW View structures and data on thermotropic liquid crystals Liquid Crystal Group Hamburg, Univ. Hamburg http://liqcryst.chemie.uni-hamburg.de/ 76,000
(free full data for 5,000)
- (yes) (common abbre-
viation)
yes - - yes (full data set not on Web, must be purchased) yes - - - - - -
Spectra Online View spectral data Thermo Galactic http://spectra.galactic.com/SpectraOnline/ 26,000
spectra
yes - yes - yes - (only for viewing spectra) - yes - - - - - -
Search & Source Purchase samples ChemNavigator http://www.chemnavigator.com/ 1,900,000 - yes - yes - (SLN, SD,
via 
cut & paste)
yes yes
(trial free)
yes - (yes -
only for paying members)
- (to NCI - only for paying members) - -
SPECnet Purchase samples SPECS and BioSpecs B.V. https://www.specsnet.com/user/ 175,000 (?) - yes yes - - (yes - SPECS-IDs) yes (Guest login avail.) - yes - yes: SD - - RS3 Structure Display -
ChemDiv Purchase samples ChemDiv, Inc. http://www.chemdiv.com 260,000 - yes - - - - yes - yes - - yes - - SS crashed Netscape
4.76
ChemFinder View properties, purchase compounds CambridgeSoft http://chemfinder.cambridgesoft.com/ 75,000 yes yes yes - yes -
(only to get plugin)
- yes yes (only CDX, C3D) - yes Chem3D
(registr. required)
-
Available Chemicals Xchange (ACX) Obtain structure and data of, purchase, compounds CambridgeSoft  http://www.chemacx.com >250,000 yes yes yes - yes - (only for purchasing) - yes - yes (multi- structure SD-files) (vendor catalog details) ChemDraw Net -
NCI DB View structures and data of Open NCI DB compounds CambridgeSoft http://nci.chemfinder.com 247,000 yes yes yes - yes - - - ?? ?? ?? ?? ?? ChemDraw Net Searches didn't yield any result
ChemExper Chemical Directory (CCD) Retrieve & submit(!) structures & data University of Lausanne http://www.chemexper.com/ 40,000 yes yes yes yes yes - - - yes yes yes - -
(only w/o structures)
(Chem3D optional) -
SPRESI View structures and literature references InfoChem http://www.infochem.de/spresiwebframe.htm
(also accessible through ChemWeb.com)
4,000,000 - yes - - - - yes yes
(free trial)
yes - - - - - -
ACD Find commercially available compounds MDL through ChemWeb.com:
http://www.chemweb.com/databases,
then select "ACD The Available Chemicals Directory" (user-specific URL, login required)
varying numbers given, 240,000 - 315,000 yes yes yes - yes - yes for full record access yes yes - - - ISIS Draw;
Chime
-
various: NMR spectra, pKa, LogP Obtain physicochemical data, spectra ACD Labs through ChemWeb.com:
http://www.chemweb.com/databases,
then select desired ACD Labs database (user-specific URL, login required)
varies by DB: 3,600 ... >100,000 - yes - - - - yes - yes - - - - ISIS Draw;
Chime
-
Bretherick's Reactive Chemicals Hazards DB Obtain hazard information Butterworth Heinemann through ChemWeb.com:
http://www.chemweb.com/databases,
then select Bretherick's DB (user-specific URL, login required)
5,000 yes yes yes - yes - yes - yes - - - - ISIS Draw;
Chime
-
CRC Combined Chemical Dictionary Obtain general reference information Chapman & Hall through ChemWeb.com:
http://www.chemweb.com/databases,
then select CRC CCD (user-specific URL, login required)
450,000 yes yes yes - yes - yes - yes - - - - ISIS Draw;
Chime
-
Negwer Obtain use and synonym data FIZ Chemie Berlin through ChemWeb.com:
http://www.chemweb.com/databases,
then select Negwer (user-specific URL, login required)
13,000 yes yes yes - yes - yes - yes - - - - ISIS Draw;
Chime
-
JHC Article Database Search for articles (back to 1963) Journal of Heterocyclic Chemistry http://217.170.33.74/ 177,000 (but dupl. between articles) yes (yes) ("key-
word")
- - - yes - - - - - - - SS search non-
functional
Sigma-
Aldrich Catalog
Retrieve catalog data Sigma-Aldrich http://www.sigma-aldrich.com/saws.nsf/
ProductSearch?OpenFrameset
200,000 yes yes yes - yes - (some structures) - (some) - - - - ISIS Draw, Kekule, or ChemDraw;
SAFWeb.exe
-
Acros Catalog Retrieve catalog data, order samples Acros Organic http://www.acros.be/ 17,000 chemicals yes yes yes yes yes - yes - yes yes yes (catalogs down- loadable) - Chime optional Ctalog PDF files didn't work

Explanation of columns:

Number of molecules
The approximate number of molecules offered through the service (usually according to the web site).

Formula search
Search by molecular formula possible.SS search
Search by (sub-)structure possible.

Name search
Search by chemical name (and/or name fragments) possible.

SMILES search
Search by SMILES string possible.

CAS-RN search
Search by CAS Registry Number possible.

Upload search file
The user can upload a file with a whole list of search criteria. Typically, this will be simple identifiers, such as a list of CAS-RNs.

Registration necessary
The user has to register, typically by choosing a user ID and a password, to use some or all of the features of the web site. This does not necessarily imply fees, by may require the user to provide personal data.

Fees
Fees may be levied for use of some or all the features and/or data on the web site. Free trial accounts may be available.

2D display
The structures found in the search are displayed as a two-dimensional drawing, i.e. a "normal" chemical structure. This may be in the form of just a graphics file (such as GIF), which can't be further processed as a chemical structure information; or it may be as an input string to one of the chemical display plugins such as Chime and others.

3D display
The structures found in the search are, or optionally can be, displayed as a three-dimensional model (the 3D coordinates being experimental or calculated - typically the latter). This usually requires the use of a plugin such as Chime, RasMol etc.

Save/export structure
The user can save (export) individual structures that resulted from the search (or browsing) in the database in a computer-readable format (.mol [SD file], .pdb, SMILES etc.) useful for further user-side processing.

Bulk download
The user can download substantial parts of the database (ideally up to the entire database), or at least the raw data that went into building the web service, in bulk format, such as multi-structure SD files.

External links
The web site offers links from individual search results (structures) to other web services that may have additional information, and/or processing capabilities for this compound. A typical example would be linking, via the CAS-RN, to PubMed for searching for literature mentioning this compound; or linking to services that may calculate spectra. Links within the service to other pages with additional capabilities and processing options do not count as external links in this context.

Plugins needed
This lists the web browser plugins that may be needed, or useful, for using the site. Typically, these are plugins for drawing and/or displaying chemical structures.

Problems encountered
Here we list problems we experienced when testing the site. This does not mean that the problem is with the site itself (could be our hardware or software setup, or simply our mistakes); or that, if it was, it hasn't been fixed in the meantime. It only means that we did encounter the problem when we used the site, and we list it here in case this information may be useful for users. But it also doesn't mean, if there is a "-" in this column, that the site is guaranteed to be error-free...

We chose not to include, as separate table columns, a number of "advanced features" such as 3D pharmacophore search capability, substructure search with atom and bond attributes, search by structural features such as number of H-bond donors/acceptors, number of stereocenters, and quite a few others more. We did not encounter such capabilities virtually anywhere else (than in our site, see second table row), and therefore inclusion in the table would only have created a lot of additional empty columns.

M. C. Nicklaus

Last Update: 2015-07-29