September 21, 2011

September 21, 2011
Gamers Solve Molecular Puzzle


Welcome to another day in my life. Today is Wednesday and we have almost made it through another work week. Dab the AIDS Bear and I are still dealing with the current situations.

I do want to share some exciting news I read about how gamers have supposedly solved the puzzle to the molecular structure of HIV. Here is the story as reported:

Video-game players have solved a molecular puzzle that stumped scientists for years, and those scientists say the accomplishment could point the way to crowdsourced cures for AIDS and other diseases.

"This is one small piece of the puzzle in being able to help with AIDS," Firas Khatib, a biochemist at the University of Washington, told me. Khatib is the lead author of a research paper on the project, published today by Nature Structural & Molecular Biology.

The feat, which was accomplished using a collaborative online game called Foldit, is also one giant leap for citizen science a burgeoning field that enlists Internet users to look for alien planets, decipher ancient texts and do other scientific tasks that sheer computer power can't accomplish as easily.

"People have spatial reasoning skills, something computers are not yet good at," Seth Cooper, a UW computer scientist who is Foldit's lead designer and developer, explained in a news release. "Games provide a framework for bringing together the strengths of computers and humans."

Unraveling a retrovirus For more than a decade, an international team of scientists has been trying to figure out the detailed molecular structure of a protein-cutting enzyme from an AIDS-like virus found in rhesus monkeys. Such enzymes, known as retroviral proteases, play a key role in the virus' spread and if medical researchers can figure out their structure, they could conceivably design drugs to stop the virus in its tracks. The strategy has been compared to designing a key to fit one of Mother Nature's locks.

The problem is that enzymes are far tougher to crack than your typical lock. There are millions of ways that the bonds between the atoms in the enzyme's molecules could twist and turn. To design the right chemical key, you have to figure out the most efficient, llowest-energy configuration for the molecule the one that Mother Nature herself came up with.

That's where Foldit plays a role. The game is designed so that players can manipulate virtual molecular structures that look like multicolored, curled-up Tinkertoy sets. The virtual molecules follow the same chemical rules that are obeyed by real molecules. When someone playing the game comes up with a more elegant structure that reflects a lower energy state for the molecule, his or her score goes up. If the structure requires more energy to maintain, or if it doesn't reflect real-life chemistry, then the score is lower.

More than 236,000 players have registered for the game since its debut in 2008.

The monkey-virus puzzle was one of several unsolved molecular mysteries that a colleague of Khatib's at the university, Frank DiMaio, recently tried to solve using a method that took advantage of a protein-folding computer program called Rosetta. "This was one of the cases where his method wasn't able to solve it," Khatib said.

Fortunately, the challenge fit the current capabilities of the Foldit game, so Khatib and his colleagues put the puzzle out there for Foldit's teams to work on. "This was really kind of a last-ditch effort," he recalled. "Can the Foldit players really solve it?"

They could. "They actually did it in less than 10 days," Khatib said.

One floppy loop of the molecule, visible on the left side of this image, was particularly tricky to figure out. But players belonging to the Foldit Contenders Group worked as a tag team to come up with an incredibly elegant, low-energy model for the monkey-virus enzyme.

"Standard autobuilding and structure refinement methods showed within hours that the solution was almost certainly correct," the researchers reported in the paper published today. "Using the Foldit solution, the final refined structure was completed a few days later."

Khatib said the Seattle team's collaborators in Poland were in such a celebratory mood that they insisted on organizing a simultaneous champagne toast, shared over a Skype video teleconference.

"Although much attention has recently been given to the potential of crowdsourcing and game playing, this is the first instance that we are aware of in which online gamers solved a longstanding scientific problem," Khatib and his colleagues wrote.

The parts of the molecule that formed the floppy loop turned out to be of particular interest. "These features provide exciting opportunities for the design of retroviral drugs, including AIDS drugs," the researchers said.

Looking for new problems to solve The monkey-virus puzzle solution demonstrates that Foldit and other science-oriented video games could be used to address a wide range of other scientific challenges ranging from drug development to genetic engineering for future biofuels. "My hope is that scientists will see this research and give us more of those cases," Khatib said.

He's not alone in that hope. "Foldit shows that a game can turn novices into domain experts capable of producing first-class scientific discoveries," Zoran Popovic, director of University of Washington's Center for Game Science, said in today's news release. "We are currently applying the same approach to change the way math and science are taught in school."

That's something that Carter Kimsey, program director for the National Science Foundation's Division of Biological Infrastructure, would love to see happen. "After this discovery, young people might not mind doing their science homework," she quipped.

One caveat, though: Playing Foldit isn't exactly like playing Bejeweled. "Let's be honest, proteins aren't the sexiest video game out there," Khatib told me. Give the game a whirl, and let me know whether it's addictive or a drag.

I will conclude this article in the blog tomorrow.

Until we meet again; here's wishing you health, hope, happiness and just enough.

big bear hug,



Daddy Dab