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Related Concept Videos

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-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 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,...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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: Jun 22, 2026

Identifying Protein-protein Interaction Sites Using Peptide Arrays
07:44

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

Identifying protein-protein interaction sites using covering algorithm.

Xiuquan Du1, Jiaxing Cheng1, Jie Song1

  • 1The Key Laboratory of Intelligent Computing and Signal Processing, Ministry of Education, Anhui University, Anhui, China.

International Journal of Molecular Sciences
|July 1, 2009
PubMed
Summary
This summary is machine-generated.

A novel covering algorithm accurately predicts protein-protein interface residues using sequence profiles and accessible area. This method offers a robust and efficient approach for identifying protein interaction sites in structural biology.

Keywords:
covering algorithmmaximum entropyprotein-protein interactionresidue accessible areasequence profile

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Last Updated: Jun 22, 2026

Identifying Protein-protein Interaction Sites Using Peptide Arrays
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Published on: November 18, 2014

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
08:38

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells

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Identification of Protein Interacting Partners Using Tandem Affinity Purification
10:02

Identification of Protein Interacting Partners Using Tandem Affinity Purification

Published on: February 25, 2012

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Identifying protein-protein interface residues is essential for understanding protein functions and interactions.
  • Existing prediction methods may lack efficiency or accuracy for high-dimensional biological data.

Purpose of the Study:

  • To propose and evaluate a covering algorithm for predicting protein-protein interface residues.
  • To assess the algorithm's performance against established machine learning methods.

Main Methods:

  • Utilized a covering algorithm incorporating protein sequence profile and residue accessible area features.
  • Employed 5-fold cross-validation on 61 protein chains for performance evaluation.
  • Compared results with Support Vector Machine (SVM) and Maximum Entropy models.

Main Results:

  • The covering algorithm achieved comparable performance to SVM and Maximum Entropy.
  • Overall accuracy reached 69.62% on the Complete dataset and 60.86% on the Trim dataset.
  • Achieved a correlation coefficient (CC) of 0.2893 and 58.83% specificity on the Complete dataset.

Conclusions:

  • The covering algorithm is a powerful and robust method for predicting protein-protein interaction sites.
  • This method can effectively guide experimental studies in structural biology.
  • The algorithm's effectiveness is validated by examining predictions within 3D protein structures.