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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...
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 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 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.
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...

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Related Experiment Video

Updated: May 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

Predicting protein-protein interface residues using local surface structural similarity.

Rafael A Jordan1, Yasser El-Manzalawy, Drena Dobbs

  • 1Department of Computer Science, Iowa State University, Ames, IA 50011, USA. rjordan@iastate.edu

BMC Bioinformatics
|March 20, 2012
PubMed
Summary
This summary is machine-generated.

Predicting protein-protein interface residues is crucial for drug discovery. The PrISE computational method uses local structural similarity to identify these residues, showing competitive performance with existing state-of-the-art approaches.

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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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Related Experiment Videos

Last Updated: May 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

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

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Drug discovery

Background:

  • Protein-protein interactions are key targets in drug discovery.
  • Interface residues are often conserved among homologous proteins.
  • Predicting these residues is a significant challenge.

Purpose of the Study:

  • Introduce PrISE, a novel computational method for predicting protein-protein interface residues.
  • Leverage local structural similarity for enhanced prediction accuracy.

Main Methods:

  • Represent protein surface residues as structural elements (central residue + neighbors).
  • Utilize atomic composition and accessible surface area within structural elements.
  • Compare structural elements to identify similar ones in a repository.
  • Develop PrISEL (local similarity), PrISEG (general similarity), and PrISEC (combined similarity) predictors.

Main Results:

  • PrISEC outperforms PrISEL and PrISEG in predicting interface residues.
  • PrISEC demonstrates competitive performance against state-of-the-art structure-based methods.
  • Local surface structural similarity alone, as used by PrISEC, achieves performance comparable to or better than global homolog-based methods like PredUs.

Conclusions:

  • Local surface structural similarity provides a simple, efficient, and effective approach for predicting protein-protein interface residues.
  • The PrISE family of methods, particularly PrISEC, offers a valuable tool for computational biology and drug discovery.