In a way this is a taster, as we’re looking at our Search as part of the refresh of ChemSpider, and more detail will follow. Another motivation for posting was a couple of recent requests for ChemSpider functionality which is already available – a great pointer to how we think about offering massive functionality in a clear interface. The two requests? One was that it would be great if a user could do a search from an input image (so to load an image, convert to structure and launch a search). The other wanted a way to just look for compounds with a specific element included. Both of these can be done on ChemSpider – and tragically both came in as amonymous feature requests. So, because I don’t think they’ve even been fully itemised before, let me count the ways by which you can search ChemSpider.

Simple Search on ChemSpider








1. Search by name – systematic name, synonym, trade name
2. Search by chemical identifier – InChI, InChIKey, SMILES
3. Search by database identifier – registry number

Structure Search on ChemSpider













4. Search by exact structure drawn, substructure, similarity – exact match, all tautomers, same skeleton (including/excluding H), all isomers
5. Draw an exact structure – in one of several structure drawers

Load a structure file from an image





6. Load from mol, sdf, skc, cdx files
7. Load from an image of the structure – gif, png, jpg, tiff – to get an editable/correctable structure for search

Convert an identifier to search ChemSpider





8. Convert an identifier or name to a structure, to use or amend in the structure search

Advanced search options in ChemSpider








9. Search for compound with/without a particular element or elements
10. Search by properties – molecular formula, mol wt, nominal mass, average mass, monoisotopic mass. Exact match or within a range
11. Search by calculated properties range – ACD/LogP, ACD/LogD (pH 5.5), ACD/LogD (pH 7.4), Rule Of 5, Number of Hydrogen Bond Acceptors, Number of Hydrogen Bond Donors, Number of Freely Rotatable Bonds, Polar Surface Area, Polar Surface Area, Molar Volume, Refractive Index, Boiling Point, Flash Point, Density, Surface Tension
12. Search by data sources – select one or many individual data sources (from the 400 we hold), one or many data source types from Available Chemicals Databases, Biological Properties , Chemical Reactions, Chemical Safety Data , Drugs or Compounds in Development, Imaging Agents , Information Aggregators, Journal Publishers via MeSH , Ligand/binding/crystal Structure Databases, Metabolic Pathways , Molecular Libraries Screening Center Network, Natural Products, NIH Substance Repository, Patents, Personal Collections, Physical Properties (including SAR/QSAR databases), Protein 3D Structures, Publication or Magazine Article, Spectroscopy Databases , Substance Vendors, Theoretical Properties, Toxicology/Environmental Databases, Virtual Library, Web-based Article (blog or commentary)
13. Search by focussed library – Building Blocks, Screening Compounds, Building Stock, D-EXP014, Acetylcholinesterase (AChE), cAMP dependent protein kinase (PKA), Estrogen Receptor (Alpha), Phospholipase A2 (PLA(2)), Test Set for DILI modelling, Test Set for DILI modelling, Training Set for DILI modelling
14. Search by ligand screening – LASSO (Ligand Activity in Surface Similarity Order) similarity
15. Combine search to look for Single- or multi-component structures
16. Combine search to look for, or disregard, isotopically labelled structures
17. Filter results with analytical data

ChemSpider APIs



18. Use our web services for mass spectrometry to search by molecular mass or elemental composition within ChemSpider or within particular data sources,
19. Use our web services to search by chemical identifier, retrieve information about ChemSpider record, retrieve the chemical structure thumbnail
20. Use our web services for spectra to return all Open Data spectral information from ChemSpider, return spectral information on a compound, return identified spectra
21. You can show all spectra of a particular type on the spectra page

Stumble it!

2 Responses to “How many ways to search ChemSpider?”

  1. James McKenzie says:

    Do you have a facility to search against both mass and chemical shifts? Obviously it would require the NMR spectrum to be uploaded and converted to a peak list. Such a facility would be really useful for spectral identification in complex mixtures, where masses and chemical shifts are strongly correlated.

  2. Antony Williams says:

    We do not have the ability to search against both mass and chemical shifts I’m afraid. As an NMR jock and structure elucidation specialist by training I agree that it would be a very useful approach. It would require every structure to have associated spectra, 26 million chemicals in total and at present we have around 2000 spectra only. So, it would require prediction of spectra across the database, storage and search methods for querying shifts and mass. It’s all technically feasible except we don’t have access to NMR prediction technology to generate 1D H1 and C13 spectra cross the entire database unfortunately.

Leave a Reply