Drug Scientists Slow to Adopt Open Source - ' Low'

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-Cost Molecular Modeling">
PyMOL models the three-dimensional structure of proteins. That can help scientists understand disease and design better drugs.

Many new drugs work by binding to proteins. By helping researchers see how a potential drug molecule nestles into the nooks and crannies of a specific protein molecule, PyMOL can help researchers imagine how to improve the drug or choose among different drug molecules based on how well each fits with proteins. According to the company's Web site, the software has been downloaded over 100,000 times.

Companies that download PyMOL are free to use it as a starting point to develop their own proprietary modifications. And though Delano dreams of communities of chemists and computer programmers contributing modules to make PyMOL more robust, too few have materialized. Other open-source products include Jmol, Chemistry Development Kit, Adaptive Poisson-Boltzmann Solver, Molecular Modelling Toolkit and GROMACS.

Plenty of code gets written at pharmaceutical companies, but they are reluctant to allow such work to be shared, said session organizer Andrew Smellie, senior investigator at cancer therapeutic company ArQule. The industry is "fanatic about IP [intellectual property] and it spills over not just to their [drug] compounds but to the rest of their business," he said.

That attitude could change as information technology becomes more integrated with drug discovery and development, hinted Rozwell, particularly because many biopharmaceutical companies feel they've made big investments in IT with little to show for it.

In addition, she said, some companies are trying to figure out how to use, rather than simply protect, intellectual property. "If you just have a patent, and you're not doing anything with it, it actually is not an asset anymore," she said. "So if you're managing your IP [intellectual property] well, you're a good candidate for [thinking about] open source."

Rozwell thinks something similar is already occurring when biopharmaceutical companies are highly involved in improving software vendors' products. The end result is similar to open source, she said. "It's a collaboration that will not only improve a product for the purchaser but that will benefit the whole industry."

An example of this was also presented at the conference. Daniel McMasters, senior research chemist at Merck, described adapting subscription-based software from Spotfire so that biologists could readily compare data across different types of assays, classes of chemical compounds and even individual test runs.

The Spotfire project began with frustrated biologists, who felt that existing techniques to summarize data hid crucial information about how cells responded to varying concentrations of different drugs.

"Every Friday, the biologists were looking at curves all day, highlighting data they didn't trust," recalled McMasters. So he and his team tweaked the program to reduce "artifacts of data reduction." For example, if separate assays measuring a drug's efficacy showed incompatible results, the program readily allowed researchers to drill down into individual test runs to look for anomalies.

Though the Spotfire staff participated in the project, it hadn't anticipated this particular use, said McMasters. Now, he said, it should be available to others.

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