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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,...
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...
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: May 15, 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

Protein interface classification by evolutionary analysis.

Jose M Duarte1, Adam Srebniak, Martin A Schärer

  • 1Paul Scherrer Institut, Villigen, CH-5232, Switzerland.

BMC Bioinformatics
|December 25, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces a novel computational method using evolutionary data and core residue analysis to accurately distinguish biologically relevant protein interfaces from crystal contacts. The approach significantly improves the prediction of protein-protein interactions, advancing structural biology.

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Last Updated: May 15, 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

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

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Distinguishing biologically relevant protein-protein interfaces from crystal contacts is a persistent challenge in structural biology.
  • Existing computational methods for predicting interface character have limitations.

Purpose of the Study:

  • To develop and validate a novel protein-protein interface classifier.
  • To accurately differentiate biologically relevant interfaces from non-biological lattice contacts.

Main Methods:

  • Utilized evolutionary data, including sequence entropy of homolog sequences.
  • Incorporated a geometric measure: the number of core residues (fully buried residues >95% burial).
  • Employed stringent quality filtering of structural and sequence data, and conservative selection of homolog sequences.

Main Results:

  • The number of core residues is a powerful discriminator of interface character.
  • Combined geometric and evolutionary measures achieved high accuracy in distinguishing biological from crystal interfaces.
  • A conservative selection of homolog sequences yielded a clearer evolutionary signal.

Conclusions:

  • An evolutionary approach is crucial for advancing the prediction of protein interface character.
  • The developed method achieves 89% accuracy on the Ponstingl 2003 dataset.
  • The software is available as a web interface (http://www.eppic-web.org) for structural biology and bioinformatics applications.