By Randall Osborne

West Coast Editor

Almost a year to the day after its second round, GeneFormatics Inc. raised $22 million in its third round of financing to advance the company¿s structural proteomics work.

The San Diego-based firm also said it has put together a strategic partnership with three of the new investors ¿ Bruker AXS Inc., Bruker BioSpin Corp. and Bruker Daltonics Inc. ¿ for analysis of 3-dimensional protein structures and the supply of research infrastructure systems.

¿They were definitely a package deal [in the financing],¿ said John Schmid, chief financial officer of GeneFormatics. The trio of Bruker companies is associated with the founding firm, Bruker NMR, in Bellerica, Mass.

Through the deal, GeneFormatics and the Brukers will develop three experimental technologies deployed by GeneFormatics in its Diamond structural proteomics platform, to investigate protein targets faster.

GeneFormatics bills its approach to identifying protein targets ¿function first,¿ using in silico methods to find protein functions, prioritizing them even before 3-dimensional analyses or other investigations are done. The company seeks all-important data on sequences and how they fold, using what it calls Fuzzy Functional Form technology to get at ¿predictive¿ functions.

¿The concept of function first is somewhat obvious, but in fact, that isn¿t the traditional approach to structural proteomics,¿ Schmid said. ¿We use structural intermediates, and then double back for experimental work on a substantially narrowed target list.¿

So far, GeneFormatics has analyzed most of the publicly disclosed human protein sequences, as well as the entire proteomes of several human pathogens and model organisms, making more than 10,000 structural and functional discoveries.

¿[During] our first run-through of the public-domain sequences in humans, several months ago, we did on the order of less than 30 days, 25,000 sequences,¿ Schmid told BioWorld Today. ¿Then, we triage down the number of sequences we think are novel and worthwhile targets.¿

Scientists claim the human genome contains 3,000 to 10,000 druggable targets, he noted. ¿The question is: Who¿s going to get at them the fastest?¿ Schmid said.

Other new investors in this round are TaKaRa Shuzo Co., of Shiga, Japan; China Development Industrial Bank, of Taipei, Taiwan. Earlier investors taking part in the third round are the Perseus-Soros BioPharmaceutical Fund LLP, of New York; Merrill Lynch Ventures, of New York; Orbimed Advisors LLC, of New York; Burrill & Co., of San Francisco; GeneChem Inc., of Montreal; Inglewood Ventures, of San Diego; and Moss Forest Venture, of Madison, Miss.

At the first of this year, GeneFormatics merged with Structure Function Genomics LLC, of Princeton, N.J., adding more firepower to its 3-dimensional analysis of proteins, and a worldwide license agreement with Rutgers University for other structural genomics technologies. (See BioWorld Today, Jan. 18, 2001.)

¿We didn¿t need to complete a financing at this time, but we were able to, because of the quality of the science and the [intellectual property] estate we¿re building,¿ Schmid said, adding that disclosure of another participant in the financing will follow shortly, along with news of a new collaboration.

The other financing entity is in a quiet period as required by SEC rules.

¿We¿ve been in a little bit of a quiet period¿ ourselves in the past three or four months,¿ Schmid added.