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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 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...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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 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...

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Related Experiment Video

Updated: Jun 16, 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

A fast indexing approach for protein structure comparison.

Lei Zhang1, James Bailey, Arun S Konagurthu

  • 1National ICT Australia Victoria Research Laboratory, The University of Melbourne, Melbourne, Victoria, Australia. lzhan@csse.unimelb.edu.au

BMC Bioinformatics
|February 4, 2010
PubMed
Summary
This summary is machine-generated.

A new algorithm, IR Tableau, dramatically speeds up protein structure comparison. This method achieves significant speedups and comparable accuracy, enabling large-scale analysis of protein structure databases.

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Last Updated: Jun 16, 2026

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

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Published on: November 3, 2011

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

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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
  • Bioinformatics
  • Computational Biology

Background:

  • Protein structure comparison is crucial in structural biology.
  • Current methods for searching large protein structure databases are slow.
  • There is a need for faster and accurate protein structure comparison techniques.

Purpose of the Study:

  • To develop a novel algorithm for rapid protein structure comparison.
  • To enhance the efficiency of searching large protein structural databases.
  • To maintain high accuracy in protein structure matching.

Main Methods:

  • Developed the IR Tableau algorithm for protein tertiary structure comparison.
  • Utilized the tableau representation for structural comparison.
  • Employed information retrieval-based feature indexing techniques for comparing tableaux.

Main Results:

  • IR Tableau achieves a two-orders-of-magnitude speedup compared to existing methods.
  • Experimental analysis on the ASTRAL SCOP database confirms high matching accuracy.
  • The algorithm demonstrates significant performance improvements for protein structure searches.

Conclusions:

  • Information retrieval-based indexing enables substantial speedups in protein structure comparison.
  • The IR Tableau algorithm offers strong comparison accuracy.
  • This approach facilitates large-scale processing of extensive protein structure databases.