InforMax has taken a "significant step into functional proteomics," by acquiring exclusive distribution rights to AxCell Biosciences’ Inter-Functional Proteomic database, said Steve Lincoln, senior vice president of life science informatics at InforMax.
InforMax will integrate the IFP database with its GenoMax platform. The companies will preview the new application at the CHI Genome Tri-Conference March 3-9 in San Francisco.
While the IFP database marks InforMax’s first proteomics offering, "it certainly won’t be the only one," said Lincoln, who said the company intends to make the GenoMax platform capable of representing the full range of complex cellular systems.
InforMax joins a number of companies hailing the recent publication of the human genome sequencing papers as a signal to concentrate their bioinformatics efforts beyond sequencing and toward gene and protein function.
"Now we’re really starting to play in the endgame," Lincoln said. "We’re starting to shift our emphasis from how do we get the whole genome done to what do we do now that it’s done."
Lincoln said the partnership with AxCell is InforMax’s first step in that direction.
Under the three-year collaboration agreement, AxCell and InforMax are developing a Protein-Protein Interaction module for GenoMax that will allow users to incorporate public, proprietary, and third-party genomics and proteomics data with the IFP database.
The IFP database contains protein-protein interaction data that AxCell compiled in its wet lab research. "The value of that data is very strong. However, the utility becomes even greater when you use that data in conjunction with existing public genomic and proteomics data as well as proprietary data," said Brian Bullard, CIO of AxCell Biosciences.
The companies expect the product to be commercially available in the second quarter of this year.
The GenoMax Protein-Protein Interaction Module will allow users to access and visualize the IFP data through several features. These include a Graphical Affinity Matrix Viewer to identify the matrix of protein interactions and a Protein Network Viewer to identify specific protein interaction pathways.
The PPI module will also offer the ability to filter, sort, and cluster data to target specific relationships and permit users to save selected protein networks into the database for analysis.
Lincoln said that AxCell’s protein data is unique because it provides detailed functional information about how the proteins interact. This level of detail forced InforMax to meet new computational challenges in its design of the PPI.
"It’s driven us to more of a super-set functionality," Lincoln said.
Bullard said that AxCell chose InforMax over a number of potential distribution partners who he declined to name.
"When we saw the initial demo of the GenoMax software, our laboratory scientist came into my office and said, ‘That’s how I think,’" Bullard said. "None of the other software out there garnered that reaction from the scientists that work here at AxCell."
The IFP database will be updated regularly, though Bullard said the frequency has not yet been determined. AxCell intends to completely chart the protein-protein interactions for the entire human proteome within two to four years.
AxCell has already mapped all the interactions of the WW protein domain, and is currently working on the PDZ and SH3 domains. The human proteome is estimated to contain between 60 and 80 such domains.
"Our throughput is constantly increasing," said Bullard, "and we have plans to expand and increase that throughput further."
Lincoln said that InforMax is in talks with several other proteomics and pathways analysis companies as it continues its efforts to expand the GenoMax platform beyond DNA-level genomics.