Nanotechnology online: gamers invited to aid protein design

Nanotechnology online: gamers invited to aid protein design

Can online gamers add to the nanotech toolkit for perfecting the de novo design of proteins that do not exist in nature? Prof. David Baker, who shared the 2004 Foresight Institute Feynman Prize in Nanotechnology in the Theoretical category, and whose milestone work in the protein engineering pathway to productive nanosystems was noted here two months ago (Major nanotechnology milestone: protein catalysts designed for non-natural chemical reactions), has invited online gamers to help develop better protein structures. Excerpts from “Biologists Enlist Online Gamers“, at Technology Review, written by Katherine Bourzac:

…The potential payoffs of making proteins that don’t exist in nature, such as those needed for HIV vaccines or as catalysts for more-efficient biofuel production, are huge. But making proteins to meet a specific need can be difficult.

Now a leading protein researcher has teamed up with computer scientists to create an online game for developing useful protein structures. David Baker, a leading protein scientist at the University of Washington, says that players will help his lab design new vaccines and make enzymes for repairing DNA in diseased tissues.

…Baker recently demonstrated the first algorithm for building novel, functioning enzymes from scratch. But while proteins built from the ground up may have chemical properties unmatched by anything in nature, they aren’t particularly efficient.

The game, called Foldit, is part of Baker’s vision for the future of protein engineering. His algorithms are good at the nitty-gritty of generating completely novel protein sequences for a particular purpose. But humans, who are better at seeing the big picture than computers are, could improve computer-designed proteins by playing the game.

…Since 2005, Baker’s lab has relied on the computing power of Internet users who’ve installed a program that searches through protein designs. About 200,000 people around the world run his Rosetta@home program when their computers would otherwise be idle. As Rosetta@home runs, it displays the protein structures that it’s processing as a screen saver. Some users staring at the structures, which look like large tangles of multicolored string, told Baker that they could see how to make the structure better—where to tuck in a loose end, or how to pull the structure together tighter—but were frustrated because they had no way to provide input.

…The first several levels of Foldit are designed to teach players what good proteins look like and how to manipulate them using the tools of the game.

…After improving the designs of a few test proteins, players can advance into competitive play, working in teams or alone. Baker and [game designer Zoran] Popović have set players to work on proteins whose structures are known in order to refine the game and train a group of players. In time, players will be working on new HIV vaccines and Baker’s other projects.

…By making the game available to anyone over the Web, the researchers expect to find people they call protein savants—people who are very good at solving protein structures and who will spend several hours a week playing the game.

If you think you might be a protein savant, or would like to become one, you can download the Foldit game for free. Perhaps you will eventually get to work on a structure on the path to productive nanosystems.

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  1. […] Dr. David Baker, who with Dr. Brian Kuhlman was awarded the 2004 Foresight Nanotech Institute Feynman Prize for Theory, will be one of three winners of the 2008 Raymond and Beverly Sackler International Prize in Biophysics. Dr. Baker has been featured on Nanodot posts this year for inviting online gamers to aid in protein design and for the design of protein catalysts for non-natural chemical reactions. From the University of Washington, via AAAS EurekAlert “Protein folding researcher David Baker to receive Sackler Prize in Biophysics“ […]

  2. […] than four years ago we asked here whether online gamers playing Foldit could help perfect the de novo design of proteins that do not […]

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