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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 9, 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

iLoops: a protein-protein interaction prediction server based on structural features.

Joan Planas-Iglesias1, Manuel A Marin-Lopez, Jaume Bonet

  • 1Structural Bioinformatics Laboratory, Universitat Pompeu Fabra, 08003 Barcelona, Spain.

Bioinformatics (Oxford, England)
|July 12, 2013
PubMed
Summary
This summary is machine-generated.

iLoops is a new web server that predicts protein-protein interactions using local structural features. It helps identify interacting protein pairs, addressing a limitation in current bioinformatics tools.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Protein-protein interactions are fundamental to numerous biological processes.
  • Predicting these interactions is crucial but current tools are limited.
  • A new web server, iLoops, has been developed to address this need.

Purpose of the Study:

  • To introduce iLoops, a novel web server for predicting protein-protein interactions.
  • To utilize local structural features for interaction prediction.
  • To provide an accessible tool for researchers studying protein interactions.

Main Methods:

  • iLoops accepts protein sequences and pairs to be tested as input.
  • Structural features are assigned to proteins based on sequence similarity.
  • A random forest classifier evaluates interaction likelihood using feature pairs (loops or domains).

Main Results:

  • The server predicts the likelihood of interaction between protein pairs.
  • It classifies feature pairs based on their presence in known interacting and non-interacting proteins.
  • The method leverages local structural information for prediction.

Conclusions:

  • iLoops offers a new method for predicting protein-protein interactions.
  • The server uses local structural features and a random forest classifier.
  • It enhances the available resources for studying protein interaction networks.