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Predicting protein structures with a multiplayer online game.

Nature | Aug 5, 2010

People exert large amounts of problem-solving effort playing computer games. Simple image- and text-recognition tasks have been successfully 'crowd-sourced' through games, 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 methodology, 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.

Pubmed ID: 20686574 RIS Download

Mesh terms: Algorithms | Computational Biology | Computer Graphics | Computer Simulation | Cooperative Behavior | Cues | Games, Experimental | Group Processes | Humans | Hydrogen Bonding | Hydrophobic and Hydrophilic Interactions | Imaging, Three-Dimensional | Internet | Leisure Activities | Models, Molecular | Nuclear Magnetic Resonance, Biomolecular | Photic Stimulation | Problem Solving | Protein Conformation | Protein Folding | Proteins | Stochastic Processes | Thermodynamics

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This is a list of tools and resources that we have found mentioned in this publication.


PyMOL

A user-sponsored molecular visualization software system on an open-source foundation. The software has the capabilities to view, render, animate, export, present and develop three dimensional molecular structures.

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PDB

A worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids. It contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. The RCSB PDB curates and annotates PDB data according to agreed upon standards. The structures in the archive range from tiny proteins and bits of DNA to complex molecular machines like the ribosome. Users can perform simple or complex queries on the data and analyze and visualize the results. FTP and Web services are also available. RCSB PDB staff are located at Rutgers, the State University of New Jersey and the University of California, San Diego.

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