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Related Concept Videos

Protein Folding01:22

Protein Folding

Overview
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding01:22

Protein Folding

Overview
Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Algorithm discovery by protein folding game players.

Firas Khatib1, Seth Cooper, Michael D Tyka

  • 1Department of Biochemistry, University of Washington, Box 357370, Seattle, WA 98195, USA.

Proceedings of the National Academy of Sciences of the United States of America
|November 9, 2011
PubMed
Summary
This summary is machine-generated.

Players in the online game Foldit developed novel protein folding algorithms through collaborative gameplay. These player-discovered strategies rivaled and even surpassed scientific methods, demonstrating the power of citizen science in scientific discovery.

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Area of Science:

  • Computational Biology
  • Biophysics
  • Citizen Science

Background:

  • The game Foldit enables players to collaboratively build protein structure models.
  • Player solutions sometimes exceed state-of-the-art computational methods for complex protein folding problems.
  • Understanding how collaborative gameplay generates effective strategies is crucial for computational applications.

Purpose of the Study:

  • To investigate if high-performing Foldit player strategies could be codified and formalized for computer use.
  • To explore the social evolution of player-developed algorithms within the Foldit framework.

Main Methods:

  • Foldit gameplay mechanics were enhanced with tools for players to create and share "recipes" encoding their folding strategies.
  • Over 5,400 unique recipes were developed through creation, modification, and recombination by players.
  • The most successful recipes were identified and analyzed for their algorithmic content.

Main Results:

  • A rapid social evolution of player-developed folding algorithms occurred after the introduction of recipe-sharing tools.
  • Two dominant recipes emerged, containing algorithms strikingly similar to an unpublished algorithm developed concurrently by scientists.
  • Benchmark calculations confirmed that the independently discovered algorithms outperform existing methods.

Conclusions:

  • Online scientific game frameworks like Foldit can solve complex scientific problems.
  • These platforms have the potential to discover and formalize novel strategies and algorithms through collective intelligence.
  • Citizen science participation can lead to significant advancements in computational methods for scientific research.