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Related Concept Videos

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-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...
Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
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...
Protein Folding01:22

Protein Folding

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Updated: Jun 23, 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-protein docking dealing with the unknown.

Irina S Moreira1, Pedro A Fernandes, Maria J Ramos

  • 1REQUIMTE, Departamento de Química, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 687, Porto 4169-007, Portugal.

Journal of Computational Chemistry
|May 23, 2009
PubMed
Summary
This summary is machine-generated.

Protein-protein docking predicts complex structures, crucial for drug discovery. This review covers docking algorithms, protein flexibility, and biological insights for improved accuracy and wider application.

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Protein Target Prediction and Validation of Small Molecule Compound
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Protein Target Prediction and Validation of Small Molecule Compound

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Protein Target Prediction and Validation of Small Molecule Compound
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Protein Target Prediction and Validation of Small Molecule Compound

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Area of Science:

  • Structural biology
  • Computational biochemistry
  • Bioinformatics

Background:

  • Protein-protein interactions are vital in biological processes.
  • Understanding complex 3D structures aids biochemical and pharmacological studies.
  • Protein-protein docking algorithms have advanced significantly.

Purpose of the Study:

  • To review the principles governing protein-protein docking.
  • To discuss search and scoring algorithms (the docking problem).
  • To explore the use of protein flexibility and biological information (hot spots) in docking.

Main Methods:

  • Review of existing computational docking algorithms.
  • Analysis of search and scoring strategies.
  • Examination of methods incorporating protein flexibility and hot spot data.

Main Results:

  • Docking algorithms have progressed but face challenges for widespread use.
  • Search and scoring are key components of the docking problem.
  • Incorporating flexibility and biological information can enhance docking accuracy.

Conclusions:

  • Protein-protein docking is essential for inferring function and guiding experiments.
  • Further refinement of algorithms, flexibility, and biological data integration is needed.
  • This review provides insights into current docking principles and software.