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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...
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 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

Scoring functions for protein-protein interactions.

Iain H Moal1, Rocco Moretti, David Baker

  • 1Joint BSC-IRB Research Program in Computational Biology, Life Science Department, Barcelona Supercomputing Center, C/ Jordi Girona 29, 08034 Barcelona, Spain.

Current Opinion in Structural Biology
|July 23, 2013
PubMed
Summary
This summary is machine-generated.

Computational methods for protein-protein interactions are crucial for analyzing high-throughput data. Recent advances and future applications in structural and energetic evaluation aid in understanding binding, sequence, and structure relationships.

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
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Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells

Published on: March 3, 2015

Related Experiment Videos

Last 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

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
08:38

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells

Published on: March 3, 2015

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Biophysics

Background:

  • High-throughput initiatives generate vast amounts of data on protein-protein interactions.
  • Understanding these interactions is key to deciphering biological functions.
  • Existing computational tools focus on structural and energetic properties.

Purpose of the Study:

  • To review recent developments in computational protein-protein interaction evaluation.
  • To discuss future applications and areas needing further investigation.
  • To explore how different computational challenges are interrelated.

Main Methods:

  • Quantifying structural and energetic properties of interacting proteins.
  • Utilizing functions for loop modeling, side-chain refinement, docking, and multimer assembly.
  • Applying methods for affinity prediction, mutation effects, hotspot identification, and interface design.

Main Results:

  • Information from models optimized for one task benefits others.
  • Interrelated challenges include sequence, structure, and binding free energy.
  • Multi-task learning and Pareto-optimal multi-objective learning frameworks can unify diverse applications.

Conclusions:

  • Computational evaluation of protein-protein interactions is vital for managing large biological datasets.
  • Synergistic use of computational models across various challenges enhances understanding.
  • Further research integrating multi-task and multi-objective learning is warranted.