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Related Concept Videos

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
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 and Protein Structure02:15

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...

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Related Experiment Video

Updated: May 29, 2026

Scalable Nanohelices for Predictive Studies and Enhanced 3D Visualization
08:03

Scalable Nanohelices for Predictive Studies and Enhanced 3D Visualization

Published on: November 12, 2014

PackHelix: a tool for helix-sheet packing during protein structure prediction.

Chengcheng Hu1, Patrice Koehl, Nelson Max

  • 1Department of Computer Science University of California, Davis, California 95616, USA.

Proteins
|September 10, 2011
PubMed
Summary

This study presents a novel method for predicting protein structures by generating native-like packings of alpha-helices onto beta-sheets. The approach ensures accurate protein structure prediction by focusing on the geometric arrangement of these key structural elements.

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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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

Related Experiment Videos

Last Updated: May 29, 2026

Scalable Nanohelices for Predictive Studies and Enhanced 3D Visualization
08:03

Scalable Nanohelices for Predictive Studies and Enhanced 3D Visualization

Published on: November 12, 2014

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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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

Area of Science:

  • Structural biology
  • Computational biology
  • Protein folding

Background:

  • Protein three-dimensional structure is determined by the packing of secondary structure elements like alpha-helices and beta-strands.
  • Accurate protein structure prediction relies on predicting the topology and geometry of these motifs.
  • Generating native-like packings of helices onto sheets remains a challenge in computational protein modeling.

Purpose of the Study:

  • To develop a computational method for generating the packing of multiple alpha-helices onto a given beta-sheet for alpha/beta sandwich protein folds.
  • To improve the accuracy of protein structure prediction by addressing the challenge of helix-sheet packing.

Main Methods:

  • Utilized statistical analysis of alpha/beta(2) motifs in known protein structures to derive geometric attributes for helix-sheet packing.
  • Employed a geometric builder that samples these attributes to generate multiple helix arrangements on a beta-sheet.
  • Incorporated consistency checks for loop geometry, collision minimization, and hydrophobic core formation.

Main Results:

  • The developed method successfully generates packings of multiple helices on a beta-sheet.
  • Generated protein structures achieved root-mean-square deviation (RMSD) values within 4-6 Å of the native structure.
  • The method's accuracy is maintained irrespective of the number of helices being packed.

Conclusions:

  • The new method provides a robust approach for modeling helix-sheet packing in alpha/beta sandwich proteins.
  • This contributes to more accurate protein structure prediction, particularly for complex folds.
  • The ProteinShop module offers a valuable tool for computational structural biology research.