All fired up

LONDON—Equinox Pharma Ltd. in mid-December launched a Web portal with a pay-per-use (PPU) version of Equinox's bioinformatics software, Phyre. Phyre, which stands for Protein Homology/analogy Recognition Engine, is used to predict protein structures.

 

The PPU software extends a continuum of Phyre products to suit various researchers' needs, says Riccardo M. Bennett-Lovsey, business development director at Equinox.

 

"Our main product is the Phyre-Server, which is an extensive system designed to run as a Web-server (either in-house or remotely) and can process structure predictions in parallel across large-scale Linux farms. The interfaces have been designed to be user-friendly for non-experts, but flexible enough for specialists to use effectively."

 

Equinox first trimmed Phyre-Server to Phyre-Lite, which runs from a command line on Linux systems. Phyre PPU, says Bennett-Lovsey, runs like Phyre-Server and has advanced options, including controlling job progress, deleting or restarting jobs  and submitting batch jobs. All can be monitored through a Web interface.

Equinox's goal is to make Phyre accessible to scientists who aren't knowledgeable about computers or even protein bioinformatics. Phyre PPU was designed to work on the familiar Google paradigm, says Bennett-Lovsey: the user pastes in a sequence, and Phyre returns potential matches from its database.

To find the most accurate matches, Phyre draws on a complete library of known proteins, says Bennett-Lovsey, before, if necessary, using de novo modeling for predicting protein structures from scratch. De novo modeling is the basis of Equinox's Phragment package for predicting protein structures from small fragments. Equinox plans to release Phragment soon and also has in silico logic-based drug discovery technology.

Equinox believes Phyre's PPU version should appeal to small or medium-sized companies or other researchers whose intermittent use of Phyre doesn't justify purchasing full licenses. Inquiries have come from biotech and pharma as well as the cosmetics and food industries.

"A single submission to the Phyre server costs between 25 and 45 pounds, depending on how many you purchase," says Bennett-Lovsey, referring to Equinox's internal credit system.

 

Companies also save time: they can begin analyzing proteins immediately rather than waiting for licenses and contracts. "It just gives a lot more flexibility," says Bennett-Lovsey.

Jonathan Witonsky, manager and industry analyst for drug discovery technologies and clinical diagnostics at Frost & Sullivan, also sees flexibility in Phyre PPU.

 

"The technology," says Witonsky, "provides a clever alternative to software tools that are often prohibitively costly to pharmaceutical and biotechnology companies. The 'pay as you go' model is likely to become popular with the wide contingent of users who are tired of bioinformatics solutions that require frequent updates. Moreover, the EQUINOXppu.com Web portal gives flexibility to researchers whose varying needs don't demand constant access to protein fold recognition software."

Equinox plans to incorporate additional bioinformatics applications into its PPU portal.

 

"We aim to consolidate as much as we can for our users," says Bennett-Lovsey, so scientists needn't worry about negotiating licenses or costs. Equinox will contract with universities and institutions whose applications are often restricted to noncommercial research. Equinox is familiar with expanding uses for industry: Phyre was developed at Imperial College London, and three Imperial College professors founded Equinox. The college's Phyre site is for academic use and directs commercial users to Equinox's site, which refers to Phyre-Server as "an enhanced version of Phyre."