SAN DIEGO--GeneFormatics, a new bioinformatics company here, was expected to announce the hiring of its first CEO at Bioinform press time. With that post filled, the company will have much of its senior management team in place, and will soon finalize its board of scientific advisors, company officials said last week.
"Now we're moving from virtual mode to real mode in the past month and a half," said Jacquelyn Fetrow, the company's chief scientific officer and one of four Scripps Research Institute scientists who founded it. In May, GeneFormatics licensed from Scripps the sequence- and structure-based function prediction methods that the four researchers--Fetrow, Adam Godzik, Andrzej Kolinski, and Jeff Skolnick--had developed.
GeneFormatics' initial strategy is to focus largely on contract research because prospective clients want proprietary sequences, said John Schmid, CFO. Subscription-based services for non-proprietary sequences will also be available.
With large quantities of protein sequence data from various genome sequencing projects becoming available, GeneFormatics plans to help companies identify the important targets in the "vast sea" of protein sequences, said Fetrow. She distinguished between other approaches--what she called sequence-only methods--and that of GeneFormatics.
The sequence-only technique examines a sequence and performs sequence alignment or sequence motif matching and then tries to equate sequence with function, Fetrow explained. GeneFormatics, on the other hand, inspects sequences and predicts function using a "structural intermediate." The company goes from sequence to structure to function first, predicting the structure of the protein using the proprietary algorithms licensed from Scripps. Then it identifies functional sites in predictive models, again using the Scripps technology. This technology, described in papers published in the Journal of Molecular Biology, allows GeneFormatics to identify between 10 and 30 percent more sequences than the standard sequence alignment and sequence motif methods, claimed Fetrow.
"It also has the advantage of using structure, which allows you to identify, or at least predict, on the protein structure where the actual functional sites lie. This should give pharmaceutical and ag biotech companies a leg up on product development," she explained. GeneFormatics' descriptors of enzyme active sites, termed Fuzzy Functional Forms, will provide informatics techniques that are faster, simpler, more sensitive, and more accurate than current methods, the company contended.