Opening some eyes

ChemZoo online database brings in OpenEye software

Lloyd Dunlap
SANTA FE, N.M. & RALEIGH, N.C.—The ChemSpider service, which currently offers chemists access to a database of nearly 18 million compounds, with text and structure/substructure searching capabilities, will be enhanced by incorporating a number of OpenEye Scientific Software Inc. products based on a licensing agreement between OpenEye and ChemZoo Inc.
ChemZoo was incorporated in 2007 by founder and president Anthony Williams to provide protection against any unforeseen but nevertheless possible litigation resulting from development and use of the ChemSpider database. Williams, who recently retired as CSO of ACD/Labs, established ChemSpider as a free-access Web site.
 
"I started the service with part-time workers and no revenue," he notes, "but it has developed a lot of interest." Currently, he adds, the database is visited by 3,000 chemists per day and has received an additional 600,000 compounds in the past two weeks. Built solely around small molecules, he believes ChemSpider is the largest chemistry database in the world.

"We intend for ChemSpider to offer the fastest chemical structure searches available online and delivered with the flexibility and usability necessary to encourage repeat usage," Williams states. "There are tens, if not hundreds, of chemical structure databases and no single way to search across them. There are databases of curated literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data and on and on. The only way to know whether a specific piece of information is available for a chemical structure is to have simultaneous access to all of these databases. Since many of these databases are for profit there is no way to easily determine the availability of information within these commercial or even in the open access databases."

With ChemSpider, the intention is to aggregate into a single database all chemical structures available within open access and commercial databases and to provide pointers from the ChemSpider search engine to the information. The service will allow either access the data immediately via open access links or have the information necessary to continue searches into commercially available systems. Accessing the information may require a commercial transaction with the provider, Williams notes.

Dr. Matthew Stahl, senior vice president at OpenEye, notes that, "Most of what we do is write software that pharma uses to identify and optimize leads. Our tool kits facilitate proper handling of chemical names, chemical structures and chemical reactions."

OpenEye's Lexichem has already been used to generate IUPAC names for compounds in the ChemSpider repository. In the future, Lexichem will also be used to convert IUPAC or other chemical names provided by users of the ChemSpider site into chemical structures in real time. Other OpenEye tools will provide 2D depictions of chemical structures, calculate physicochemical properties for compounds in the ChemSpider repository, and allow the normalization of protomeric and tautomeric forms.

"We've allowed the academic community free access to our products for 10 years," Dr. Stahl notes, "This new partnership is fully in line with that philosophy: Chemists from around the globe will now have free access to a central repository with efficient data-mining and rendering tools, partly powered by our technology."
 

Lloyd Dunlap

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