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Structural Bioinformatics Partners with ChemNavigator to Boost In Silico Screening

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Structural Bioinformatics has forged its first alliance with a cheminformatics company. Last week, SBI and ChemNavigator signed a collaborative agreement under which SBI and its customers will have access to ChemNavigatior’s 3D database of two million drug-like compounds.

Under the terms of the agreement, SBI and its Genes to Leads service customers — who include BioChem Pharma, Yamanouchi Pharmaceutical, Kirin, and DuPont — will be able to screen chemical compounds in the ChemNavigator database in silico against the 2,600 3D proprietary protein structures in SBI’s drug target database.

SBI and ChemNavigator will share in revenues generated from the combined use of their technologies. Further financial terms of the agreement were not disclosed.

“What we get with the ChemNavigator relationship is really an eight-fold expansion of the chemical space that can be provided to us,” said Ed Maggio, CEO of SBI.

SBI’s Gene to Leads technology uses a proprietary technique called augmented homology modeling to convert sequence data into 3D protein structures. The computational method is far more rapid than x-ray crystallography, but provides protein structures that are comparable in quality, according to Maggio.

While conventional homology modeling produces models that differ from x-ray structures by about 5 angstroms, Maggio said that SBI’s method creates models that are about 1.5 angstroms RMS deviation from a corresponding x-ray structure.

SBI then draws on collections of small molecules like the ChemNavigator collection to predict molecules with drug activity.

Using this approach, Maggio said, “Instead of getting hit rates as seen in high-throughput screening of one in a hundred thousand or one in ten thousand, we get hit rates of one in ten.”

Maggio predicted that similar combinations of computational and empirical methodologies would soon become general practice in the pharmaceutical industry.

“It will never be done all computationally, but the days of doing it entirely empirically are gone now,” Maggio added.

— BT

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