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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 24, 2026

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

Progress and challenges in predicting protein-protein interaction sites.

Iakes Ezkurdia1, Lisa Bartoli, Piero Fariselli

  • 1Centro Nacional de Biotechnolgia, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.

Briefings in Bioinformatics
|April 7, 2009
PubMed
Summary

Predicting protein-protein interaction sites is crucial for protein network analysis. Current methods show improvement but face challenges with data availability and standardization for reliable predictions.

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Identifying Protein-protein Interaction Sites Using Peptide Arrays
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Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
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Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells

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Related Experiment Videos

Last Updated: Jun 24, 2026

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

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

Identifying Protein-protein Interaction Sites Using Peptide Arrays

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

Published on: March 3, 2015

Area of Science:

  • Biochemistry and Molecular Biology
  • Computational Biology
  • Structural Biology

Background:

  • Identifying protein-protein interaction sites is vital for understanding cellular processes, enabling mutant design, and predicting protein networks.
  • Numerous computational methods have emerged for predicting interface residues, necessitating a review of the field's current state.

Purpose of the Study:

  • To review the current methodologies, datasets, and evaluation procedures for predicting protein-protein interaction sites.
  • To analyze the impact of various features and algorithms on prediction accuracy.
  • To identify persistent challenges and suggest future directions for the field.

Main Methods:

  • Analysis of existing computational methods for predicting protein-protein interaction sites.
  • Evaluation of feature sets and algorithms commonly used in prediction models.
  • Assessment of data set generation and analysis protocols.

Main Results:

  • While prediction methods have improved, significant bottlenecks persist, particularly concerning the under-representation of protein complexes in structural databases.
  • Challenges in generating reliable datasets and performing robust posterior analyses were highlighted.
  • The impact of specific features and algorithms on prediction performance was analyzed.

Conclusions:

  • Progress in predicting protein-protein interaction sites is hindered by data limitations and the lack of standardized evaluation metrics.
  • Effective feature selection strategies are proposed.
  • Community-wide standards for training, testing, and performance measurement are essential for advancing the field.