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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 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.
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 Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

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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

PRISM: protein-protein interaction prediction by structural matching.

Ozlem Keskin1, Ruth Nussinov, Attila Gursoy

  • 1Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Istanbul, Turkey.

Methods in Molecular Biology (Clifton, N.J.)
|July 2, 2008
PubMed
Summary

Prism predicts protein-protein interactions using a novel structure-based algorithm. This system identifies potential new interactions by analyzing protein structures and evolutionary data, aiding biological discovery.

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Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Protein-protein interactions (PPIs) are fundamental to cellular processes.
  • Predicting PPIs is crucial for understanding biological functions.
  • Existing methods often lack accuracy or scalability.

Purpose of the Study:

  • To introduce Prism, a novel system for predicting protein-protein interactions.
  • To leverage structural and evolutionary information for enhanced prediction accuracy.
  • To provide a user-friendly platform for exploring predicted PPIs.

Main Methods:

  • Developed a bottom-up prediction algorithm combining structural and sequence conservation of protein interfaces.
  • Utilized a database of 3799 nonredundant protein interface structures from the Protein Data Bank (PDB).
  • Predicted interactions among 6170 proteins, with verification against DIP and BIND databases.

Main Results:

  • A substantial portion of predicted interactions were verified in public databases, validating the approach.
  • The system successfully identified potential novel protein-protein interactions.
  • Prism provides an interactive interface viewer and access to prediction results.

Conclusions:

  • The Prism system offers a reliable and effective method for predicting protein-protein interactions.
  • Verified interactions confirm the suitability of the structure-based approach.
  • Unverified predictions highlight potential undiscovered biological interactions.