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Related Concept Videos

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 Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
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.

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Related Experiment Video

Updated: Jul 11, 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

PPT-DB: the protein property prediction and testing database.

David S Wishart1, David Arndt, Mark Berjanskii

  • 1Department of Biological Sciences, Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada.

Nucleic Acids Research
|October 6, 2007
PubMed
Summary
This summary is machine-generated.

The Protein Property Prediction and Testing Database (PPT-DB) offers a centralized resource for protein property data, aiding in the development of prediction tools. It also enables accurate homology-based predictions, outperforming standard methods.

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Last Updated: Jul 11, 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

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances
07:35

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Published on: October 11, 2018

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Computational Biology

Background:

  • Protein property data is fragmented across numerous sources.
  • Accurate prediction of protein properties is crucial for biological research and drug development.
  • Existing methods for protein property prediction have limitations in accuracy and scope.

Purpose of the Study:

  • To create a comprehensive, centralized database of protein property data.
  • To provide a resource for developing and validating protein property prediction algorithms.
  • To enable accurate homology-based protein property predictions.

Main Methods:

  • Curated data from nearly 30 databases were integrated.
  • Structural and dynamic protein properties were collected and standardized.
  • Sequence similarity searches against the database were developed for predictions.

Main Results:

  • PPT-DB houses diverse protein properties, including structural and dynamic features.
  • Homology-based predictions achieved 85-95% accuracy for categorical data and >0.80 correlation for numerical data.
  • Predictions using PPT-DB showed a 10-20% improvement over standard 'ab initio' methods.

Conclusions:

  • PPT-DB serves as a valuable, standardized resource for protein property prediction research.
  • Homology-based prediction using PPT-DB offers superior accuracy compared to existing methods.
  • The database and its prediction utilities are freely available for use.