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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 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...

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Updated: Jun 4, 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 spectral approach to protein structure alignment.

Yosi Shibberu1, Allen Holder

  • 1Department of Mathematics, Rose-Hulman Institute of Technology, 5500 Wabash Avenue, Terre Haute, IN 47803, USA. shibberu@rose-hulman.edu

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|February 9, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces a novel spectral analysis for protein fold alignment, developing two algorithms. These methods effectively identify protein fold families and achieve high-quality alignments using intrinsic geometry.

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Last Updated: Jun 4, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
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Published on: November 3, 2011

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

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Machine learning for genomics

Background:

  • Protein structure alignment is crucial for understanding protein function and evolution.
  • Existing methods may struggle with accurately aligning distantly related protein folds.
  • A new intrinsic geometry derived from spectral analysis offers a novel approach.

Purpose of the Study:

  • To introduce a new intrinsic geometry for protein fold alignment based on spectral analysis.
  • To develop and evaluate two novel alignment algorithms utilizing this geometry.
  • To demonstrate the effectiveness of these algorithms in identifying protein fold families.

Main Methods:

  • Development of a mathematically rigorous intrinsic geometry based on scaled distance matrices and positive eigenvalues.
  • Implementation of a first alignment algorithm using eigenvalues and dynamic programming for rapid fold alignment.
  • Extension to a second algorithm that iterates between intrinsic and 3D protein geometry for high-quality alignments.

Main Results:

  • The first algorithm achieved efficient protein fold alignment and family identification on the Skolnick40 and Proteus300 datasets.
  • The second algorithm produced high-quality alignments for challenging protein fold comparisons.
  • The second algorithm demonstrated strong performance in correctly identifying fold families across benchmark datasets.

Conclusions:

  • The novel spectral analysis and intrinsic geometry provide a powerful framework for protein fold alignment.
  • The developed algorithms offer improved accuracy and efficiency in identifying protein fold families.
  • This approach advances the field of structural bioinformatics and protein structure comparison.