By Matthew Willett

Proteomics player GeneFormatics Inc. said its second round of financing grossed $15 million, funding it will use to ramp up its technology platform, a move the company¿s CEO says is appropriate in what could be termed a land-grabbing phase for the industry.

The Series B financing, led by the Perseus-Soros BioPharmaceutical Fund LP, included new investors Merrill Lynch Ventures, OrbiMed Advisors and GeneChem Management. Existing investors, including Burrill & Co., Inglewood Ventures and Moss Forest Venture, also participated in the round.

Perseus-Soros Managing Director Christopher Earl will join the company¿s board of directors as a part of the financing.

¿Proteomics is a hot space right now,¿ GeneFormatics CEO John Chiplin said. ¿As we get into the post-genomics era the challenge for any company in proteomics is to ramp up as fast as possible, and with the success we¿ve already had, the sentiment here is to turn up the gas and build the technology platform as soon as possible.¿

Chiplin said the San Diego company will use the funding to seek alliances and licenses for technology to complement its protein structure and functional analysis of genomic data platform, which uses a proprietary library the company calls Fuzzy Functional Forms.

¿What we have is a hybrid sequence stroke structure approach,¿ he said. ¿There¿s a lot of technology to determine function that focuses on 1-dimensional sequence data. What we¿re doing is building a platform that looks at sequences and how they fold.

¿As people sequence genes they¿re finding proteins that, in large part, they can¿t determine the function of. What our technology can do is go through the sequence very rapidly and determine the function.¿

The process begins with a rapid folding of the protein in question. The structural design produced is approximate, he said, but sufficient for the company¿s purposes.

¿We use a special version of a protein data bank, taking the 3-dimensional motifs and flexize them ¿ this is where the term fuzzy,¿ comes in ¿ and search the structure with those flex motifs. Basically, we end up with a predictive function of a protein, and we¿ve done a lot of work validating this. We can dig deeper, and get 30 to 40 percent more hits, more function, with our method than with the typical.¿

He said the company will pursue partnerships for technology that will solidify its position in the industry.

¿Right now what we have is a proprietary platform for mining protein sequences and determining protein function from 1-dimensional sequences. We¿ll be using some of the funds to invest in our platform to build it more quickly. We feel there¿s a lot of technology around that area that could add value and true synergy to the existing platform, so we¿re talking to other technology collaborators.¿

The company already collaborates with some big names. Both Schering-Plough Corp., of Madison, N.J., and Bristol Myers Squibb Co., of New York, have partnered with GeneFormatics, seeking functional analysis of proprietary protein sequences.

Chiplin said he hopes to place his company in the upper echelon of proteomics in the future through financings like this one, and he doesn¿t discount a public offering as a potential funding mechanism.

¿The combination of in silico methods with other methods used in structural genomics, that¿s a true synergy. We¿ll be evaluating technology over the course of the next couple of months, evaluating it late this year and early next year. Proteomics is so hot and in the early stages, it¿s the company that can build critical mass the quickest that will be the Celera [Genomics] or the Millennium [Pharmaceuticals Inc.] of the proteomics generation, the ones that build bulk quickly.¿

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