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Pharmacopeia s Software Divisions MSI and GCG to Build Integrated Database Architecture

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Molecular Simulations, a division of Pharmacopeia based in San Diego, Calif., demonstrated a new relational database of annotated protein sequences and structures at its recent Functional Genomics Consortium meeting.

The database, called AtlasStore, integrates data from MSI’s GeneAtlas functional annotation tool with the SeqStore bioinformatics package offered by Genetics Computer Group, MSI’s sister division, which was recently acquired by Princeton, N.J.-based Pharmacopeia.

Both GeneAtlas and AtlasStore are available exclusively to members of MSI’s Functional Genomics Consortium, which recently gained two new members: Both Genaissance Pharmaceuticals and Argentina’s GEMA (Grupo de Estudios Multicéntros en Argentina) joined founding members Cytoclonal Pharmaceutics and Hyseq over the past few weeks.

Consortium members pay an undisclosed fee for a three-year term in exchange for exclusive access to the technology. David Edwards, director of the consortium, said that an initial version of AtlasStore is currently being installed at member sites. Other consortium members are in the pipeline as well, Edwards said.

Edwards said the consortium would next move toward incorporating more information about protein families and chemistry within the database.

MSI and GCG, based in Madison, Wis., intend to work closely together to build a single platform to provide information on protein sequence and structure, chemistry, and genomic data. “We’ve been mapping out a strategy over the last several months,” Edwards said.

AtlasStore will serve as a single architecture that will help Pharmacopeia integrate its software tools, Edwards said.

Through its recent acquisitions of MSI, GCG, Oxford Molecular Group, and Synopsys Scientific Systems, Pharmacopeia now offers a range of software for bioinformatics and cheminformatics. “Functional genomics really sits right in between the two,” Edwards said. “We’re trying to take the data from bioinformatics and turn it into information that then gives you a lead onto what sort of chemistry to look at.”

Some observers have interpreted the flurry of acquisitions, along with the company’s recent decision to create two separate COO positions for its software and drug discovery businesses, as a move toward integrating the four software companies into a single unit.

A Pharmacopeia spokeswoman did not return calls for comment on the company’s plans for its software business.

—BT

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