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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 Organization01:24

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 Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
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...
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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Updated: May 13, 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

New enumeration algorithm for protein structure comparison and classification.

Cody Ashby1, Daniel Johnson, Karl Walker

  • 1Molecular Bioscience Graduate Program, Arkansas State University, Arkansas, USA.

BMC Genomics
|March 1, 2013
PubMed
Summary
This summary is machine-generated.

We developed an efficient algorithm for protein structure comparison using secondary structure elements. Our method, ePC, significantly improves computational efficiency and identifies biologically relevant substructures.

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Last Updated: May 13, 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

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

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:

  • Computational Biology
  • Bioinformatics

Background:

  • Protein structure comparison aids in understanding protein structure-function relationships.
  • This comparison is computationally intensive.
  • Many methods utilize secondary structure elements (SSEs) for protein structure representation.

Purpose of the Study:

  • To investigate the complexity of protein structure comparison using a mixed-graph model.
  • To develop an efficient computational approach for protein structure comparison.

Main Methods:

  • Developed an effective protein structure comparison approach named ePC (efficient enumeration-based Protein structure Comparison).
  • Utilized a novel independent set enumeration algorithm within a mixed-graph model.
  • Analyzed theoretical running-time complexity, achieving O(1.47 rnn2).

Main Results:

  • The ePC approach demonstrates significantly improved theoretical running-time compared to other graph-based methods.
  • Tested ePC for general protein structure comparison and specific protein examples.
  • The algorithm effectively identifies substructures from high-scoring solutions.

Conclusions:

  • The enumeration algorithm enables the identification of biologically interesting substructures.
  • ePC offers flexibility in comparing SSEs in both sequential and non-sequential orders.
  • Supplementary data and the ePC source code are available online.