4.8 Article

Algorithm discovery by protein folding game players

Publisher

NATL ACAD SCIENCES
DOI: 10.1073/pnas.1115898108

Keywords

citizen science; crowd-sourcing; optimization; structure prediction; strategy

Funding

  1. Center for Game Science
  2. Defense Advanced Research Projects Agency (DARPA) [N00173-08-1-G025]
  3. National Science Foundation (NSF) [IIS0811902, IIS0812590, 0906026]
  4. Howard Hughes Medical Institute
  5. Henry Wellcome Postdoctoral Fellowship
  6. Adobe
  7. Microsoft
  8. Direct For Biological Sciences
  9. Div Of Biological Infrastructure [0906026] Funding Source: National Science Foundation
  10. Div Of Information & Intelligent Systems
  11. Direct For Computer & Info Scie & Enginr [0811902] Funding Source: National Science Foundation

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Foldit is a multiplayer online game in which players collaborate and compete to create accurate protein structure models. For specific hard problems, Foldit player solutions can in some cases outperform state-of-the-art computational methods. However, very little is known about how collaborative gameplay produces these results and whether Foldit player strategies can be formalized and structured so that they can be used by computers. To determine whether high performing player strategies could be collectively codified, we augmented the Foldit gameplay mechanics with tools for players to encode their folding strategies as recipes and to share their recipes with other players, who are able to further modify and redistribute them. Here we describe the rapid social evolution of player-developed folding algorithms that took place in the year following the introduction of these tools. Players developed over 5,400 different recipes, both by creating new algorithms and by modifying and recombining successful recipes developed by other players. The most successful recipes rapidly spread through the Foldit player population, and two of the recipes became particularly dominant. Examination of the algorithms encoded in these two recipes revealed a striking similarity to an unpublished algorithm developed by scientists over the same period. Benchmark calculations show that the new algorithm independently discovered by scientists and by Foldit players outperforms previously published methods. Thus, online scientific game frameworks have the potential not only to solve hard scientific problems, but also to discover and formalize effective new strategies and algorithms.

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