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Scinova Merges QSAR Concept with Machine Learning for Bioinformatics Analysis

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Quantitative structure activity relationship (QSAR) analysis — which correlates structural features of small molecules with biological activity properties — is an old standby in computational chemistry. Now, Mumbai, India-based Scinova Informatics is applying the concept to biological data.

Scinova co-founder Rajeev Gangal said that the company is able to calculate physical, chemical, and structural properties not only for small molecules, but also for DNA and protein sequences and structures. This information, he said, can then be analyzed to make predictions about functional properties.

Gangal, a former discovery informatics scientist at AstraZeneca R&D Bangalore, founded Scinova in August 2002, along with Vishal Jajodia, CEO of organic chemical firm Euresian Group. Nine additional employees are developing the company’s core platform, called Prometheus. The platform first calculates properties for a set of input data — in the case of proteins, for example, properties such as the hydrophobicity index, molecular weight, or polarity; in the case of DNA, properties such as frequency of bases or GC content. Users then draw from a selection of algorithms to build up a customized analysis workflow.

Scinova has embarked upon an aggressive partnership strategy to link up certain components of the platform with other commercially available tools. In one partnership, London-based Inforsense will integrate the protein QSAR part of Prometheus into its KDE workflow platform. Scinova is also partnering with Chemnitz, Germany-based data-mining firm Prudential Systems, which will add new data-mining capabilities to Prometheus in exchange for Scinova’s time series analysis technology, Gangal said. In the US, Scinova is teaming up with dbExperts — a Miami, Fl., firm that offers a commercial version of PostgreSQL — to provide life science application development services.

These international partners are a key element of Scinova’s strategy, Gangal said, because it’s critical for the company to expand beyond India’s limited bioinformatics market. “There are lots of Indian companies and institutions working in bioinformatics, but Indian companies themselves do not make a lot of use of bioinformatics,” Gangal said. The reason? “Most Indian pharma companies don’t always start with a target-oriented approach… Generally they start with the chemical compound, and they try to optimize the compound against a particular disease and sell it to a big pharma in Europe or the US.”

Thus, the small-molecule QSAR components of Prometheus will be marketed to Indian pharmaceutical firms, but Scinova will need to find buyers for the full platform in Europe and the US — a daunting prospect, but one that doesn’t shake Gangal’s confidence. Although Prometheus is not yet on the market, Scinova is shooting to have “at least two to three copies” sold in the next six to nine months.

— BT

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