By Mary Welch

Claiming the collaboration is the largest such deal ever made - but declining to disclose how much money is involved - Compugen Ltd. entered a bioinformatics agreement with Warner-Lambert Co.

“I can't say exactly what the numbers are,“ said Peter Mansfield, vice president of sales and marketing for Woburn, Mass.-based Compugen Inc., “but we [will] receive multimillion dollars per year for each of the three years.“

The agreement with Parke-Davis, a division of Warner-Lambert Co., of Morris Plains, N.J., makes Parke-Davis Compugen's first partner for its Leads bioinformatics platform. Leads will provide Parke-Davis with solutions for identifying drug targets based on the analysis of expressed sequence tag (EST) and genomic databases, pattern recognition in expression results from chips and proteomics, and mutation detection and qualification.

Using the Leads platform, Compugen has identified thousands of human genes and alternatively spliced variants not previously identified in public-domain databases.

Compugen got its start from three members of the elite technology unit of the Israel Defense Forces.

The three men - Simchon Faigler, vice president of technology, Eli Mintz, president of Compugen, and Amir Natan, vice president of software development - received funding from Israel to apply their skills in computers for sequence analysis.

In 1993, with Israeli private and governmental financing, they founded Compugen and developed a hardware platform that accelerated the GCG package, already a popular DNA protein sequence analysis tool.

“Essentially, we took this DNA sequence program and made it far faster,“ said Peter Mansfield, vice president of sales and marketing. “We sold it to a number of companies, like Merck [& Co., of Whitehouse Station, N.J.] and SmithKline Beecham plc [of London]. Three years ago, we built our own software and no longer use anyone else's.“

Compugen's parent company, Compugen Ltd., is headquartered in Petach Tikva, Israel, near Tel Aviv, and has a worldwide sales and support center in Woburn, Mass., near Boston. Compugen, which has about 70 employees, designs, develops and markets bioinformatics tools for use with genomic and protein sequence data.

Compugen's hardware accelerator products use proprietary as well as industry-standard algorithms. Its products include the design and implementation of algorithms, as well as software and hardware. GenCore is the company's primary software product for executing sensitive nucleotide or protein homology searches using algorithms. Another product is GenWeb, a Web-based interface. Compugen's BioXL/G is an accelerator that speeds up heuristic and dynamically programmed algorithms. The latest product is the BioXL/P, which uses field programmable gate arrays to execute computer-intensive but very rigorous algorithms, the company said.

Patent Office To Use Technology For Searches

Compugen, which is about to open a development center in Jamesburg, N.J., has won a U.S. Department of Commerce contract to supply an automated biotechnology sequence search to the U.S. Patent and Trademark Office, to enhance the office's DNA and protein search engines.

“Every protein and DNA sequence submitted for patent will be searched and analyzed using Compugen hardware and software,“ Mansfield said.

Compugen undertook its first round of financing from Israeli investors shortly after the company was established. In 1997, it completed a $4 million private financing round with U.S. Venture Partners, of Menlo Park, Calif. Another round of Israeli financing recently closed. Mansfield said an initial public offering “depends on the market.“

Compugen's clients include Bayer Corp., of Pittsburgh; Eli Lilly and Co., of Indianapolis; Human Genome Sciences Inc., of Rockville, Md.; Incyte Pharmaceuticals Inc., of Palo Alto, Calif.; and Millennium Pharmaceuticals Inc., of Cambridge, Mass. n