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Protein Lounge Offers an Online Hangout for Multiple Data Resources

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Protein Lounge may be the only bioinformatics company that got its start in the publishing business. Samik Singh, CEO of the San Diego-based provider of biomolecular databases and online software tools, does double duty as the publisher and editor of the monthly Biotech Journal, which launched in late 2000.

“After about two years we started making a good amount of profit, so I thought it might be a good idea to make a database,” Singh said. “There was really no particular reason to do it.”

Now, six months after going live, the company offers seven different databases and has around 2,000 subscribers — although only around 500 of them are paying customers, Singh said, because Protein Lounge offers a free five-day trial period for online access to its databases and software.

With annual subscription rates starting at $250, however, the barrier to signing up once the trial expires can’t get much lower. “We tried to make the pricing similar to a journal subscription,” Singh said. “We had a choice between only a few subscribers at a high price or a lot of subscribers at a low price,” he added, pointing out that some of the company’s competitors “won’t even let you look at their data until you give them $100,000.”

Protein Lounge has its share of competitors in the information business, particularly for its pathway database, which contains 302 protein-signaling and metabolic pathways that the company’s staff of 14 biologists manually collected from the literature and public resources.

The pathway database sector is one of the few success stories in the bioinformatics market in recent years, and a growing list of companies — including Ingenuity, GeneGo, Ariadne Genomics, Jubilant Biosys, and others — have found eager buyers among pharmaceutical and biotech companies. But Singh said that in addition to its lower price, Protein Lounge’s pathway database has a few features that its competitors’ don’t.

For one thing, he said, the fact that the resource is manually curated offers an advantage over others that rely on text-mining and other automated methods. “There’s a lot of hype about text-mining tools,” he said, “but I don’t think that computers have artificial intelligence to the point where they can supersede humans yet.”

Singh said that Protein Lounge assigns two biologists to each pathway. Working simultaneously, they have no contact with one another until the pathway is complete, at which time they compare their results to ensure that they agree.

Singh said this process takes a bit longer than some of Protein Lounge’s competitors: The team can finish around 10 pathways a month compared to a few days for other pathway database companies. But “longer is better,” he said, when it comes to biological information.

Protein Lounge’s pathway database also differs visually from some of its competitors. Unlike other databases that use Java-based 2D programs to represent pathway data, Protein Lounge hired a team of three graphic designers from the video game industry to illustrate the pathways using 3D Max, the same software used to render characters in video games. Subscribers to the database can use the company’s Pathway Builder software tool to draw their own pathways. “

In addition to the pathway database, Protein Lounge offers a protein database with more than 25,000 entries; a disease gene database; a kinase-phosphatase database; and a transcription factor database with 869 entries. While these are all similar to resources available through other commercial firms or the public domain, Singh said that the company offers two additional databases that are not available from any other source: an siRNA database, which contains siRNA targets against mRNA sequences for 10 organisms; and a peptide-antigen database, which contains antigenic peptide targets against all known protein sequences.

Access to these costs an additional $225 per year.

Singh said that one reason Protein Lounge is able to keep its subscription rates so low is because most of its staff is based in India, so development costs are about a third of what they would be using US-based researchers.

But the company is exploring ways to increase its revenues through variations on its licensing model, Singh said. For example, he said, Protein Lounge is in discussions with several undisclosed reagent companies about including one or more of its databases on their websites as reference tools for prospective buyers.

In a recent agreement, Protein Lounge signed an exclusive distribution agreement with OmniViz to provide its pathway data through OminiViz’s visualization software [BioInform 09-20-04]. The company is also considering adding functionality to its website that would enable users to order reagents in the siRNA and peptide-antigen database directly from suppliers.

Singh said he’s considering adding several new database categories to the website, as well, “but we don’t want to put too much up there because it will get too cluttered,” he said. “We just want to provide the main tools that people need.”

— BT

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