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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
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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...

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Related Experiment Video

Updated: Jul 10, 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

Enhanced partial order curve comparison over multiple protein folding trajectories.

Hong Sun1, Hakan Ferhatosmanoglu, Motonori Ota

  • 1Department of Computer Science and Engineering, The Ohio State University, Columbus, OH 43210, USA. sunh@cse.ohio-state.edu

Computational Systems Bioinformatics. Computational Systems Bioinformatics Conference
|October 24, 2007
PubMed
Summary

Researchers developed a new algorithm to analyze protein folding simulations. This enhanced partial order (EPO) algorithm effectively extracts meaningful biological features from complex folding trajectory data.

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Related Experiment Videos

Last Updated: Jul 10, 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

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

  • Computational Biology
  • Molecular Dynamics
  • Biophysics

Background:

  • Protein folding is crucial for understanding molecular life.
  • Computational power generates vast amounts of protein folding simulation data.
  • Interpreting this data to find novel folding features is challenging.

Purpose of the Study:

  • To develop an effective algorithm for analyzing protein folding trajectories.
  • To extract novel and biologically meaningful features from simulation data.
  • To address challenges in comparing high-dimensional folding curves.

Main Methods:

  • Modeling folding trajectories as multi-dimensional curves.
  • Developing an enhanced partial order (EPO) algorithm for multiple curve comparison (MCC).
  • Applying the EPO algorithm to diverse folding trajectories, including successful and unsuccessful simulations.

Main Results:

  • The EPO algorithm successfully detects similarities at a low level.
  • It can extract biologically meaningful folding events from simulation data.
  • Demonstrated effectiveness in a case study with the miniprotein Trp-cage(24).

Conclusions:

  • The EPO algorithm provides an effective method for interpreting protein folding simulation data.
  • It aids in identifying novel folding features and understanding protein dynamics.
  • This approach enhances the analysis of complex molecular behavior.