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Related Concept Videos

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 Folding01:22

Protein Folding

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Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding01:22

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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 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.

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Updated: Jun 19, 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

Protein structure classification based on conserved hydrophobic residues.

Pradeep Chowriappa1, Sumeet Dua, Jinko Kanno

  • 1Data Mining Research Laboratory and the Department of Computer Science, College of Engineering and Science, Louisiana Tech University, PO Box 10348, Nethken Hall, Ruston, LA 71272, USA. pradeep@latech.edu

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|October 31, 2009
PubMed
Summary

This study introduces a novel graph-theory approach to analyze protein structures, identifying conserved hydrophobic patterns. This method accurately classifies proteins, aiding in structural and functional annotation.

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07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

  • Biochemistry and Structural Biology
  • Computational Biology and Bioinformatics

Background:

  • Protein folding is crucial for function, often driven by local residue interactions forming clusters.
  • Hydrophobic propensities of residues are key determinants of these interactions, with various scales developed to quantify them.
  • Identifying conserved structural features across evolutionary-related proteins remains a challenge.

Purpose of the Study:

  • To develop a data mining framework for extracting invariant protein structural features.
  • To leverage hydrophobicity scales and graph theory for analyzing evolutionary conserved patterns.
  • To test the hypothesis that homologous proteins share analogous residue interaction patterns.

Main Methods:

  • A graph-theory-based data mining framework was developed.
  • Integrated analysis of five established hydrophobicity scales applied to 3D protein structures.
  • Extraction of discriminatory residue interaction patterns within protein families.

Main Results:

  • Identified conserved hydrophobic residue interaction patterns in evolutionary-related proteins.
  • Demonstrated the utility of these patterns for protein structural and functional annotation.
  • Achieved an average of 90% accuracy in protein classification with a reduced feature vector.

Conclusions:

  • The proposed framework effectively extracts evolutionarily invariant structural features.
  • Conserved hydrophobic patterns are reliable indicators for protein classification and annotation.
  • This approach offers a significant improvement in accuracy and efficiency for protein analysis.