Chemical Search Engines and Databases on the Internet

CWM Global Search (AKos GmbH) - a commercial user interface for searching multiple databaseson the Internet by structure, CAS Registry Number® and Synonym. Structure search include exact, isomer, substructure and similarity searches. Supports reaction queries. Supports multiple compounds in one query. Supports SOAP interface for web-services.
The largest free databeses include: Chemical Structure Lookup Service, ChemSpider, PubChem, PubMed , eMolecules, AKos Samples, ChemExper Chemical Directory, novo|seek (question) and PubMed Central (question) (>1 mln compounds each) (Jan. 2010)
Commercial databases are from Symyx: DiscoveryGate, CIRX, JSM, ORGSYN, SPRESI, ACD, SCD, CMC, DDR, Metabolites, etc.
Note: There is unique possibility of substructure search in Chemical Structure Lookup Service (CSLS)

ChemSpider (RSC) - a free chemistry search engine for searching multiple sources by structure, chemical and trade names, CAS Registry Number, SMILES or InChI. Structure search capabilities include exact, tautomers, substructure, superstructure and similarity searches.
The largest compound sources: PubChem, PubMed, eMolecules, ZINC, ChemDB, AKos, DiscoveryGate, Thomson Pharma, Ryan Scientific (>1 mln compounds each) (Jan. 2010).
Manual (2007)
Note: Chemical Structure Lookup Service (CSLS) is not included in the list of sources.
Content: About 23 million compounds, > 200 sources (Oct. 2009)

Chemical Structure Lookup Service (CSLS): "Look up whether a structure occurs in any of tens of different databases, both public and commercial". Exact structure search (look-up) is enabled by structure formula, for InChI, SMILES, structure files in multiple formats. Search by molecular formula and IDs used in the original individual databases. InChI search allows use wildcard to retrieve different tautomers. Compound text identifiers (InChI, SMILES, etc.) could be automatically extraxted from the text and converted into query. Allows also input structures from image or PDF files using OSRA (Optical Structure Recognition) tool. Supports SOAP interface for web-services.
List of sources is not published.
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The Latest Release 11/2008: search in 74 million indexed structures from over 100 databases (46 million unique structures).

PubChem - a free database of chemical compounds deposited from multiple sources. A keyword search is possible by compound chemical name or synonims. Structure search support query input, SMILES/SMARTS, InChI, molecular formula, or SDF structure files. Structure search could be exact (identity), substructure, superstructure and similarity searches. A search query could be constructed as URL, without use a search form.
The largest contributers: ChemSpider, NextBio, DiscoveryGate, ZINC, Ambinter, ChemDB, Thomson Pharma and ChemBank (>1 mln compounds each) (Jan. 2010).
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About 26 million unique compounds (as of Jan. 28, 2010)

Commercial Sources

CAS REGISTRY (Chemical Abstracts Service, CAS) - is the gold standard for chemical substance information. Curated and quality-controlled by CAS scientists, REGISTRY includes indexed information on more than 53 million organic and inorganic substances and 61 million sequences disclosed in the world’s most reputable published sources, including many from the Web. Combine REGISTRY with the advanced search and analysis technologies in SciFinder® or the STN® family of products to find the chemical substance information you need most. To learn more, visit www.cas.org.
CAS REGISTRY Summary Sheet; Structure Searching in the CAS REGISTRY on STN; SciFinder Substructure Searching Overview
About 53 million organic and inorganic substances (as of April 30, 2010)