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Related Concept Videos

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.
Protein Organization01:13

Protein Organization

Overview
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.
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...
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...

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Related Experiment Video

Updated: May 25, 2026

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

Methods of protein structure comparison.

Irina Kufareva1, Ruben Abagyan

  • 1Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|February 11, 2012
PubMed
Summary
This summary is machine-generated.

Quantifying protein structural differences is complex. Contact-based measures are more robust than global RMSD for comparing computational models to experimental data, especially when using combined or distance-dependent methods.

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Last Updated: May 25, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
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09:51

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

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Published on: July 25, 2013

Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Comparing protein structures computationally is essential for modeling assessments.
  • Existing methods for quantifying structural differences have limitations.

Purpose of the Study:

  • To review and compare methods for assessing structural similarity between proteins.
  • To highlight the advantages of contact-based measures over traditional distance-based metrics like RMSD.

Main Methods:

  • Analysis of positional distance-based measures, including global RMSD and distance-dependent algorithms.
  • Evaluation of contact-based measures for their robustness and relevance.
  • Illustration of combined and utility-based measures.

Main Results:

  • Global RMSD is often unrepresentative of true structural similarity due to sensitivity to large errors.
  • Distance-dependent algorithms can mitigate RMSD's drawbacks.
  • Contact-based measures demonstrate greater robustness and relevance for structural comparisons.

Conclusions:

  • Contact-based measures are superior to global RMSD for quantifying protein structural differences.
  • Utilizing combined and distance-dependent measures, alongside experimental data distributions, enhances the interpretation of structural comparisons.