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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.
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...
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 and Protein Structures02:15

Protein and Protein Structures

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...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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...
Protein Folding01:22

Protein Folding

Overview

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Related Experiment Video

Updated: May 30, 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 novel method to compare protein structures using local descriptors.

Paweł Daniluk1, Bogdan Lesyng

  • 1Faculty of Physics, Department of Biophysics and CoE BioExploratorium, University of Warsaw, Żwirki i Wigury 93, Warsaw, Poland.

BMC Bioinformatics
|August 19, 2011
PubMed
Summary

A new protein structure comparison method, DEscriptor Defined Alignment (DEDAL), accurately identifies difficult similarities. This advance aids in discovering novel structural relationships and understanding molecular evolution.

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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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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

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Last Updated: May 30, 2026

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

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Protein structure comparison is crucial in bioinformatics.
  • Existing methods struggle with complex similarities like shifts, distortions, and permutations.
  • There's a need for automated systems to find subtle structural relationships.

Purpose of the Study:

  • To introduce a novel method for protein structure comparison.
  • To address limitations of current methods in identifying difficult similarities.
  • To enable discovery of previously unrecognized structural relationships.

Main Methods:

  • Developed DEscriptor Defined Alignment (DEDAL) using local structure descriptors.
  • Extended local similarities into global structural alignments.
  • Tested DEDAL on challenging benchmark datasets (SISYPHUS, SISY, RIPC).

Main Results:

  • DEDAL successfully aligned structures with non-sequential and non-rigid-body transformations.
  • Achieved 77% accuracy on the difficult RIPC set, outperforming other methods (60% accuracy).
  • Demonstrated capability in handling complex structural variations.

Conclusions:

  • DEDAL is efficient for whole-proteome analysis.
  • It can lower the threshold for detecting structure similarity, aiding molecular evolution studies.
  • Suitable for improving protein domain classification and fold space analysis.