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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 and Protein Structure02:15

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...

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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

An iterative knowledge-based scoring function for protein-protein recognition.

Sheng-You Huang1, Xiaoqin Zou

  • 1Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, USA.

Proteins
|February 6, 2008
PubMed
Summary

A new iterative method developed a knowledge-based scoring function, ITScore-PP, to predict protein-protein interactions. This efficient tool accurately identifies binding modes and correlates with binding affinities, aiding protein recognition studies.

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Computational biology
  • Structural biology
  • Biochemistry

Background:

  • Protein-protein interactions (PPIs) are crucial for cellular processes.
  • Accurate prediction of PPIs is essential for understanding biological functions.
  • Existing methods for predicting PPIs face challenges in accuracy and computational efficiency.

Purpose of the Study:

  • To develop an efficient, distance-dependent, knowledge-based scoring function for predicting protein-protein interactions.
  • To improve the accuracy of identifying true biological interfaces from decoys.
  • To provide a computationally efficient tool for protein docking and recognition studies.

Main Methods:

  • Developed an iterative method to derive interatomic pair potentials, creating the ITScore-PP scoring function.
  • Utilized a training set of 851 protein-protein dimeric complexes with true biological interfaces.
  • Tested ITScore-PP on diverse sets of protein-protein complexes, including ZDOCK and RosettaDock decoy sets.

Main Results:

  • ITScore-PP achieved high success rates in predicting native binding modes for both bound (98.9%) and unbound (40.7%) cases.
  • A residue-level variant, ITScore-PP(SCM), demonstrated strong performance (71.4% bound, 30.8% unbound).
  • ITScore-PP showed good correlation (R=0.71) with experimentally determined binding affinities.
  • The scoring function is computationally efficient, with average run times of 0.03 seconds per orientation.

Conclusions:

  • The iterative method effectively derives knowledge-based potentials, circumventing reference state problems.
  • ITScore-PP and its variant ITScore-PP(SCM) are accurate and efficient tools for predicting protein-protein interactions and binding modes.
  • These scoring functions can be integrated with protein docking software to advance the study of protein recognition.