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Related Concept Videos

Protein Folding01:22

Protein Folding

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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...
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Protein Organization01:13

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Protein Organization01:24

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Updated: May 26, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Coarse-grained model for protein folding based on structural profiles.

Katrin Wolff1, Michele Vendruscolo, Markus Porto

  • 1School of Physics, University of Edinburgh, JCMB Kings Buildings, Edinburgh EH9 3JZ, United Kingdom.

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|December 21, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces a novel coarse-grained protein model with tube-like geometry and a 1D energy function. This model accurately simulates protein dynamics and explores conformational space more efficiently than all-atom simulations.

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Last Updated: May 26, 2026

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

Published on: July 25, 2013

Area of Science:

  • Computational biology
  • Protein dynamics
  • Biophysics

Background:

  • Protein folding is complex, involving intricate interactions and conformational changes.
  • All-atom simulations are computationally expensive, limiting exploration of long timescales and large conformational spaces.
  • Coarse-grained models offer a computationally efficient alternative for studying protein dynamics.

Purpose of the Study:

  • To develop and validate a novel coarse-grained protein model.
  • To investigate protein folding dynamics and conformational landscapes.
  • To enable exploration of longer timescales in protein simulations.

Main Methods:

  • A coarse-grained protein model with tubelike geometry for self-avoidance.
  • A one-dimensional energy function based on sequence connectivity.
  • Application to the villin headpiece domain for folding behavior analysis.

Main Results:

  • The model's dynamics align well with experimental data and all-atom simulations.
  • The coarse-grained approach allows for exploration of larger conformational spaces.
  • Folding behavior, heat capacities, and free-energy landscapes were determined for villin headpiece.

Conclusions:

  • The developed coarse-grained model is a viable tool for studying protein folding.
  • This approach enhances computational efficiency for exploring protein conformational dynamics.
  • The model provides insights into the folding mechanisms of proteins like the villin headpiece domain.