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Related Concept Videos

Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Protein Folding01:22

Protein Folding

Overview
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
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...
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...

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Related Experiment Video

Updated: Jun 15, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Accounting for conformational changes during protein-protein docking.

Martin Zacharias1

  • 1Physik-Department, T38, Technische Universität München, James Franck Str. 1, Garching, Germany. martin.zacharias@ph.tum.de

Current Opinion in Structural Biology
|March 3, 2010
PubMed
Summary
This summary is machine-generated.

Computational methods are crucial for modeling protein-protein interactions when 3D structures are unknown. New flexible docking approaches improve accuracy, especially for backbone flexibility, enhancing structural modeling of protein complexes.

More Related Videos

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

Related Experiment Videos

Last Updated: Jun 15, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

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

Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • A small fraction of known protein-protein complexes have determined three-dimensional structures.
  • Computational methods are increasingly vital for modeling protein-protein interactions.
  • Current protein-protein docking methods struggle with significant conformational changes, particularly in the protein backbone.

Purpose of the Study:

  • To review and highlight advancements in computational methods for modeling protein-protein interactions.
  • To address the challenge of incorporating flexibility, especially backbone flexibility, into protein-protein docking.
  • To discuss the role of homology modeling and flexible refinement in generating accurate structural models.

Main Methods:

  • Review of emerging computational strategies for protein-protein docking.
  • Focus on flexible refinement, ensemble docking, and integrated flexibility approaches.
  • Discussion of homology modeling techniques for protein complex structures.

Main Results:

  • New computational approaches show promise in handling conformational changes during docking.
  • Flexible refinement and ensemble docking offer improved accuracy for protein complex modeling.
  • Homology modeling, combined with flexible refinement, can yield accurate structural models for many interactions.

Conclusions:

  • Advancements in flexible docking methods are essential for accurate modeling of protein-protein interactions.
  • Efficient treatment of backbone flexibility is key to improving computational protein complex prediction.
  • Computational modeling, particularly with flexible refinement, is a powerful tool for structural biology.