- 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: (U.S.) 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 to Marc Nicklaus (mn1@helix.nih.gov).
| 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: http://129.43.27.140/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://209.9.235.107/final_phase3/ | 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 |
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 a 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.
Last change: M. C. Nicklaus, 2001-10-11