Sixty-Four Free Chemistry Databases (Serialized)
The Web has created a publishing platform of unparalleled scope. Although chemistry has been slow to embrace it, the situation has shown increasing signs of change over the last few years. With the large number of new services popping up continuously, how can an interested chemist keep up?
That's where this article comes in. Every week, at least one new free chemistry database or Web resource will be profiled on Zusammen, and a link to the article will be added to this page. When sixty-four profiles have been written, the entire collection will be condensed into a single article with a short summary for each item. The result will look something like the still-popular Thirty-Two Free Chemistry Databases article on Depth-First, but with the advantage that through serialization you won't have to wait until the entire article is done to begin reading.
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We hope you find this list helpful. As always, your thoughtful feedback and suggestions make for a better finished product.
Sixty-Four Free Chemistry Databases (in progress)
- PubChem
- Sigma-Aldrich Reaction Search
- Heterocycles Web Edition
- Electronic Encyclopedia of Reagents for Organic Synthesis
- CrystalEye
- Common Chemistry
- mylims.org
- nmrdb.org
- ZINC
- Spectral Database of Organic Compounds
- Pherobase
- eMolecules
- Side Effect Resource (SIDER)
- AffinDB
- BindingDB
- WebReactions
- Organic Syntheses
- ChemSynthesis
- Symmetry@Otterbein
- Polyview 3D
- ChemSpider
- ChemMine
- Human Metabolome Database
- ChEBI
- Biochemical Pathways Database
- BRENDA
- DOCK Blaster
- ChemWiki
- NMRShiftDB
- Acronyms
- STITCH
- Spectra Online
If I may suggest some two databases from my group at EMBL: STITCH and Matador.
I'd like to mention the new RESTful interface for the Chemical Structure Lookup Service (the service is still in beta and will be part of a new CSLS version).
It allows access to any identifier available in CSLS and to convert it into another representation, e.g.:
http://cactus.nci.nih.gov/chemical/structure/CCO/inchikey
The general format of the URLS are
http://cactus.nci.nih.gov/chemical/structure/{identifier}/{method}
Allowed identifier values are: SMILES, Std. InChI/InChIKey (~50 million InChIKeys are available for lookup), chemical names (~70 million), NCI/CADD Identifier (FICuS, uuuuu), RN numbers
Methods are currently /smiles, /inchi, /inchikey, /names,/image, /ficus, /ficts, and /uuuuu but there is more to come
Some further examples:
http://cactus.nci.nih.gov/chemical/structure/CCO/names http://cactus.nci.nih.gov/chemical/structure/aspirin/image http://cactus.nci.nih.gov/chemical/structure/InChIKey=YXFVVABEGXRONW-UHFFFAOYSA-N/smiles
Rich, I'll monitor the list, and will extract those who allow deposition of user data. See Where can I host my experimental data?
Rich,
If I may add another suggestion: our SureChem patent chemistry database allows for free structure search across the full text of US, EP, and WO patents as well as all MEDLINE abstracts. This is the first and only free resource for chemical patent search.
We don't provider for deposition of data, since structures can only be extracted from patents, but will be adding a facility where users can curate SureChem data or request certain structures to be reviewed or the chemical names cleaned up (not all names currently convert to structures).
SureChem also has a paid service, SureChem Pro, which is what helps pay for SureChem Free. Both services offer access to the same data - SureChem Pro contains more powerful search tools and allow for data export.
@Michael, Markus, and Nicko - thanks for the suggestions.
For others with suggestions for free services to cover, please feel free to add them here as a comment.
Hi Rich, Thermo Scientific host a free version of their FTIRSearch.com and RamanSearch.com sites called www.spectraonline.com It allows the upload and conversion of spectra to a standard format and subsequent searching against a number of libraries. Its an under used resource an we would like to see more users taking advantage of its unique capabilities.
@David, thanks for the tip - this looks like a very useful service. Looks like the link didn't go through, so here it is: Spectra Online.
@David, after doing a search using the first example link for "Acetic Acid Using: Any Words", I got a list of results.
Unfortunately, after clicking any link, I get an error page.
My company specializes in building chemistry-focused websites. Feel free to drop me a line if you'd like to kick around some ideas for improving or promoting Spectra Online.
http://mms.dsfarm.unipd.it/MMsINC/search/
MMsINC is a database of non-redundant, richly annotated, and biomedically relevant chemical structures.
A primary goal of MMsINC is to guarantee the highest quality and the uniqueness of each entry. MMsINC then adds value to these entries by including the analysis of crucial chemical properties such as ionization and tautomerization processes, and the in silico prediction of 24 important molecular properties in the biochemical profile of each structure. MMsINC is consequently a natural input for different chemoinformatics and virtual screening applications. In addition, MMsINC supports various types of queries, including substructure queries and the novel "molecular scissoring" query.
MMsINC is interfaced with other primary data collectors such as PubChem, Protein Data Bank (PDB), the Food and Drug Administration (FDA) database of approved drugs, and ZINC.
As well I would like to mention CoCoCo, a suite of multiconformational databases especially concieved for pharmacophore virtual screenings. CoCoCo databases can be reached at the following URL and are completely free of charge: http://cococo.unimore.it