Nature, volume 466, issue 7307, pages 756-760

Predicting protein structures with a multiplayer online game

Seth Cooper ¹

Firas Khatib ²

Adrien Treuille ^{1, 3}

Janos Barbero ¹

Jeehyung Lee ³

Michael Beenen ¹

Andrew Leaver-Fay ^{2, 4}

David Baker ^{2, 5}

Zoran Popović ¹

Foldit Players

Hide authors affiliations Show authors affiliations: 5 affiliations

Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, Washington 98195, USA, |

Department of Biochemistry, University of Washington, Box 357350, Seattle, Washington 98195, USA, |

School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, USA , |

⁴

Present address: Department of Biochemistry, University of North Carolina, CB 7260, Chapel Hill, North Carolina 27599, USA., |

⁵

Howard Hughes Medical Institute, University of Washington, Box 357370, Seattle, Washington 98195, USA ,

University of Washington

Howard Hughes Medical Institute

Publication type: Journal Article

Publication date: 2010-08-03

Springer Nature

Journal: Nature

Quartile SCImago

Quartile WOS

Impact factor: 64.8

ISSN: 00280836, 14764687

DOI: 10.1038/nature09304

Copy DOI

PubMed ID: 20686574

Multidisciplinary

Abstract

A natural polypeptide chain can fold into a native protein in microseconds, but predicting such stable three-dimensional structure from any given amino-acid sequence and first physical principles remains a formidable computational challenge. Aiming to recruit human visual and strategic powers to the task, Seth Cooper, David Baker and colleagues turned their 'Rosetta' structure-prediction algorithm into an online multiplayer game called Foldit, in which thousands of non-scientists competed and collaborated to produce a rich set of new algorithms and search strategies for protein structure refinement. The work shows that even computationally complex scientific problems can be effectively crowd-sourced using interactive multiplayer games. Predicting the structure of a folded protein from first principles for any given amino-acid sequence remains a formidable computational challenge. To recruit human abilities to the task, these authors turned their Rosetta structure prediction algorithm into an online multiplayer game in which thousands of non-scientists competed and collaborated to produce new algorithms and search strategies for protein structure refinement. This shows that computationally complex problems can be effectively 'crowd-sourced' through interactive multiplayer games. People exert large amounts of problem-solving effort playing computer games. Simple image- and text-recognition tasks have been successfully ‘crowd-sourced’ through games1,2,3, but it is not clear if more complex scientific problems can be solved with human-directed computing. Protein structure prediction is one such problem: locating the biologically relevant native conformation of a protein is a formidable computational challenge given the very large size of the search space. Here we describe Foldit, a multiplayer online game that engages non-scientists in solving hard prediction problems. Foldit players interact with protein structures using direct manipulation tools and user-friendly versions of algorithms from the Rosetta structure prediction methodology4, while they compete and collaborate to optimize the computed energy. We show that top-ranked Foldit players excel at solving challenging structure refinement problems in which substantial backbone rearrangements are necessary to achieve the burial of hydrophobic residues. Players working collaboratively develop a rich assortment of new strategies and algorithms; unlike computational approaches, they explore not only the conformational space but also the space of possible search strategies. The integration of human visual problem-solving and strategy development capabilities with traditional computational algorithms through interactive multiplayer games is a powerful new approach to solving computationally-limited scientific problems.

By date By citations

Top-30

Citations by journals

	5 10 15 20 25 30
PLoS ONE	PLoS ONE, 27, 2.97% PLoS ONE 27 publications, 2.97%
Lecture Notes in Computer Science	Lecture Notes in Computer Science, 26, 2.86% Lecture Notes in Computer Science 26 publications, 2.86%
ACS Symposium Series	ACS Symposium Series, 14, 1.54% ACS Symposium Series 14 publications, 1.54%
Proceedings of the National Academy of Sciences of the United States of America	Proceedings of the National Academy of Sciences of the United States of America, 13, 1.43% Proceedings of the National Academy of Sciences of the United States of America 13 publications, 1.43%
Nature Biotechnology	Nature Biotechnology, 9, 0.99% Nature Biotechnology 9 publications, 0.99%
Nature	Nature, 9, 0.99% Nature 9 publications, 0.99%
Journal of Molecular Biology	Journal of Molecular Biology, 7, 0.77% Journal of Molecular Biology 7 publications, 0.77%
Proceedings of the ACM on Human-Computer Interaction	Proceedings of the ACM on Human-Computer Interaction, 6, 0.66% Proceedings of the ACM on Human-Computer Interaction 6 publications, 0.66%
Scientific Reports	Scientific Reports, 6, 0.66% Scientific Reports 6 publications, 0.66%
PLoS Computational Biology	PLoS Computational Biology, 6, 0.66% PLoS Computational Biology 6 publications, 0.66%
Methods in Molecular Biology	Methods in Molecular Biology, 6, 0.66% Methods in Molecular Biology 6 publications, 0.66%
Bioinformatics	Bioinformatics, 6, 0.66% Bioinformatics 6 publications, 0.66%
Journal of Medical Internet Research	Journal of Medical Internet Research, 5, 0.55% Journal of Medical Internet Research 5 publications, 0.55%
Computers in Human Behavior	Computers in Human Behavior, 5, 0.55% Computers in Human Behavior 5 publications, 0.55%
SSRN Electronic Journal	SSRN Electronic Journal, 5, 0.55% SSRN Electronic Journal 5 publications, 0.55%
Computational and Structural Biotechnology Journal	Computational and Structural Biotechnology Journal, 5, 0.55% Computational and Structural Biotechnology Journal 5 publications, 0.55%
Proteins: Structure, Function and Genetics	Proteins: Structure, Function and Genetics, 5, 0.55% Proteins: Structure, Function and Genetics 5 publications, 0.55%
F1000Research	F1000Research, 4, 0.44% F1000Research 4 publications, 0.44%
Applied Sciences (Switzerland)	Applied Sciences (Switzerland), 4, 0.44% Applied Sciences (Switzerland) 4 publications, 0.44%
Drug Discovery Today	Drug Discovery Today, 4, 0.44% Drug Discovery Today 4 publications, 0.44%
Biochemistry and Molecular Biology Education	Biochemistry and Molecular Biology Education, 4, 0.44% Biochemistry and Molecular Biology Education 4 publications, 0.44%
IEEE Access	IEEE Access, 4, 0.44% IEEE Access 4 publications, 0.44%
Science	Science, 4, 0.44% Science 4 publications, 0.44%
Journal of Microbiology and Biology Education	Journal of Microbiology and Biology Education, 4, 0.44% Journal of Microbiology and Biology Education 4 publications, 0.44%
Journal of Chemical Physics	Journal of Chemical Physics, 3, 0.33% Journal of Chemical Physics 3 publications, 0.33%
PeerJ	PeerJ, 3, 0.33% PeerJ 3 publications, 0.33%
Nature Communications	Nature Communications, 3, 0.33% Nature Communications 3 publications, 0.33%
Nature Methods	Nature Methods, 3, 0.33% Nature Methods 3 publications, 0.33%
PLoS Biology	PLoS Biology, 3, 0.33% PLoS Biology 3 publications, 0.33%
	5 10 15 20 25 30

Citations by publishers

	20 40 60 80 100 120 140 160
Association for Computing Machinery (ACM)	Association for Computing Machinery (ACM), 146, 16.08% Association for Computing Machinery (ACM) 146 publications, 16.08%
Springer Nature	Springer Nature, 134, 14.76% Springer Nature 134 publications, 14.76%
Elsevier	Elsevier, 93, 10.24% Elsevier 93 publications, 10.24%
Wiley	Wiley, 54, 5.95% Wiley 54 publications, 5.95%
IEEE	IEEE, 46, 5.07% IEEE 46 publications, 5.07%
Public Library of Science (PLoS)	Public Library of Science (PLoS), 37, 4.07% Public Library of Science (PLoS) 37 publications, 4.07%
American Chemical Society (ACS)	American Chemical Society (ACS), 33, 3.63% American Chemical Society (ACS) 33 publications, 3.63%
Taylor & Francis	Taylor & Francis, 23, 2.53% Taylor & Francis 23 publications, 2.53%
Oxford University Press	Oxford University Press, 22, 2.42% Oxford University Press 22 publications, 2.42%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 19, 2.09% Multidisciplinary Digital Publishing Institute (MDPI) 19 publications, 2.09%
Cold Spring Harbor Laboratory	Cold Spring Harbor Laboratory, 18, 1.98% Cold Spring Harbor Laboratory 18 publications, 1.98%
IGI Global	IGI Global, 14, 1.54% IGI Global 14 publications, 1.54%
Proceedings of the National Academy of Sciences (PNAS)	Proceedings of the National Academy of Sciences (PNAS), 13, 1.43% Proceedings of the National Academy of Sciences (PNAS) 13 publications, 1.43%
Frontiers Media S.A.	Frontiers Media S.A., 12, 1.32% Frontiers Media S.A. 12 publications, 1.32%
Royal Society of Chemistry (RSC)	Royal Society of Chemistry (RSC), 11, 1.21% Royal Society of Chemistry (RSC) 11 publications, 1.21%
Cambridge University Press	Cambridge University Press, 9, 0.99% Cambridge University Press 9 publications, 0.99%
Emerald	Emerald, 8, 0.88% Emerald 8 publications, 0.88%
SAGE	SAGE, 8, 0.88% SAGE 8 publications, 0.88%
Wolters Kluwer Health	Wolters Kluwer Health, 7, 0.77% Wolters Kluwer Health 7 publications, 0.77%
American Association for the Advancement of Science (AAAS)	American Association for the Advancement of Science (AAAS), 7, 0.77% American Association for the Advancement of Science (AAAS) 7 publications, 0.77%
JMIR Publications	JMIR Publications, 6, 0.66% JMIR Publications 6 publications, 0.66%
IOP Publishing	IOP Publishing, 6, 0.66% IOP Publishing 6 publications, 0.66%
Mary Ann Liebert	Mary Ann Liebert, 5, 0.55% Mary Ann Liebert 5 publications, 0.55%
Social Science Electronic Publishing	Social Science Electronic Publishing, 5, 0.55% Social Science Electronic Publishing 5 publications, 0.55%
Walter de Gruyter	Walter de Gruyter, 5, 0.55% Walter de Gruyter 5 publications, 0.55%
American Society for Microbiology	American Society for Microbiology, 5, 0.55% American Society for Microbiology 5 publications, 0.55%
Annual Reviews	Annual Reviews, 5, 0.55% Annual Reviews 5 publications, 0.55%
American Institute of Physics (AIP)	American Institute of Physics (AIP), 4, 0.44% American Institute of Physics (AIP) 4 publications, 0.44%
F1000 Research	F1000 Research, 4, 0.44% F1000 Research 4 publications, 0.44%
	20 40 60 80 100 120 140 160

We do not take into account publications without a DOI.
Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
Statistics recalculated weekly.

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Cooper S. et al. Predicting protein structures with a multiplayer online game // Nature. 2010. Vol. 466. No. 7307. pp. 756-760.

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Cooper S., Khatib F., Treuille A., Barbero J., Lee J., Beenen M., Leaver-Fay A., Baker D., Popović Z., Players F. Predicting protein structures with a multiplayer online game // Nature. 2010. Vol. 466. No. 7307. pp. 756-760.

RIS |

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TY - JOUR

DO - 10.1038/nature09304

UR - https://www.nature.com/articles/nature09304

TI - Predicting protein structures with a multiplayer online game

T2 - Nature

AU - Popović, Zoran

AU - Cooper, Seth

AU - Khatib, Firas

AU - Treuille, Adrien

AU - Barbero, Janos

AU - Lee, Jeehyung

AU - Beenen, Michael

AU - Leaver-Fay, Andrew

AU - Baker, David

AU - Players, Foldit

PY - 2010

DA - 2010/08/03 00:00:00

PB - Springer Nature

SP - 756-760

IS - 7307

VL - 466

PMID - 20686574

SN - 0028-0836

SN - 1476-4687

ER -

BibTex |

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BibTex Copy

@article{2010_Cooper,

author = {Zoran Popović and Seth Cooper and Firas Khatib and Adrien Treuille and Janos Barbero and Jeehyung Lee and Michael Beenen and Andrew Leaver-Fay and David Baker and Foldit Players},

title = {Predicting protein structures with a multiplayer online game},

journal = {Nature},

year = {2010},

volume = {466},

publisher = {Springer Nature},

month = {aug},

url = {https://www.nature.com/articles/nature09304},

number = {7307},

pages = {756--760},

doi = {10.1038/nature09304}

}

MLA

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MLA Copy

Cooper, Seth, et al. “Predicting protein structures with a multiplayer online game.” Nature, vol. 466, no. 7307, Aug. 2010, pp. 756-760. https://www.nature.com/articles/nature09304.

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Springer Nature

Journal

Nature

Quartile SCImago

Quartile WOS

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64.8

ISSN

00280836 (Print)
14764687 (Electronic)