Success Story of Collaborative Citizen Science

This is great news!  Players of the game FoldIt solved the puzzle of the molecular structure of a protein causing AIDS in rhesus monkeys that hadn’t been solved for 15 years.

The game FoldIt has been created to propose as a game the scientific problem of finding the 3D molecular structure of a protein.    Computer programs have been created to help find the 3D structure, but there are multiple possibilities, and they have to find the One and Only with minimal energy state that Nature has created :-).  But they don’t always find the right solution.  That’s what motivated scientists to create the FoldIt game. As humans are good at reducing the search space in 3D, the game presented one structure, that you can move around following the chemical rules, and your score goes up if the change is in the good direction (less energy consumption) or down if not.  The idea  is changing the molecular structure until its minimal energy state is found. It has a collaborative approach, as any gamer could leave the puzzle unfinished, and let others try it from there.

In this particular protein case, the gamers solved the puzzle in 10 days, chatting and collaborating with each other to find the solution.  A crowdsourcing success that will encourage other scientific problems to be released as games to the public.  Collaboration in times of Internet, is really a powerfull tool for innovation and discovery.

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.

University of Washington

A screen shot shows how the Foldit program posed the monkey-virus molecular puzzle.

Slide 10

Humans are very good at reducing the search space
Humans try to fold the protein into a minimal energy state.
Can leave protein unfinished and let others try from there
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