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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 Organization01:13

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...
Amino acids03:42

Amino acids

Amino acids are the monomers that comprise proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, or the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group. There are 20 common amino acids present in proteins, each with a different R group. Variation in the amino acid sequence is responsible for...

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Updated: Jun 26, 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

Structural alphabets for protein structure classification: a comparison study.

Quan Le1, Gianluca Pollastri, Patrice Koehl

  • 1Complex and Adaptive Systems Laboratory, School of Computer Science and Informatics, University College Dublin, Dublin, Ireland. quan.le@ucd.ie

Journal of Molecular Biology
|January 13, 2009
PubMed
Summary
This summary is machine-generated.

Structural alphabets approximate protein structures with motif sequences, aiding classification. Global sequences offer good approximations, improving accuracy over primary sequences but not yet replacing complex alignment methods.

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

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

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure analysis

Background:

  • Protein structure alignment is crucial for identifying shared functionality but computationally challenging.
  • Approximating protein 3D structures using sequences of structural motifs offers an alternative comparison method.

Purpose of the Study:

  • To evaluate the performance of structural alphabets for protein structure classification.
  • To compare different sequence representations (native, secondary-structure, local, and global structural sequences) for protein classification.

Main Methods:

  • Developed a structural alphabet of 20 motifs (4-residue fragments) to represent protein structures as sequences.
  • Generated local and global structural sequences from these motifs.
  • Tested four protein sequence representations with various classifiers on the CATH protein fold dataset.

Main Results:

  • Global structural sequences approximated native protein structures with an average root mean square deviation of 0.69 Å.
  • Approximation quality varied, being best for alpha-proteins and poorer for beta-proteins.
  • Structural sequence information significantly improved classification accuracy compared to native sequences, outperforming secondary-structure sequences.

Conclusions:

  • Structural alphabets provide a viable method for approximating protein structures and enhancing classification.
  • While promising, fragment-based structural sequences currently do not surpass computationally intensive structure alignment methods for protein classification.