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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...
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...
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,...

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Updated: Jun 16, 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

Flexible protein-protein docking based on Best-First search algorithm.

Efrat Noy1, Amiram Goldblum

  • 1Department of Medicinal Chemistry and the David R. Bloom Center for Pharmacy, School of Pharmacy, The Hebrew University of Jerusalem, Israel 91120.

Journal of Computational Chemistry
|January 21, 2010
PubMed
Summary
This summary is machine-generated.

We developed a novel protein-protein docking method using a Best-First search algorithm. This approach enhances binding conformation accuracy by incorporating backbone and side-chain flexibility.

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

  • Computational Biology
  • Structural Bioinformatics
  • Biophysics

Background:

  • Protein-protein interactions (PPIs) are crucial for cellular functions.
  • Accurate prediction of protein complex structures is essential for understanding biological processes.

Purpose of the Study:

  • To develop and evaluate a novel, high-resolution protein-protein docking method.
  • To assess the impact of incorporating flexibility on docking accuracy and ranking.

Main Methods:

  • A two-stage docking approach utilizing a Best-First search algorithm.
  • Stage 1: Rigid body search of unbound proteins.
  • Stage 2: Alternating rigid and flexible searches, including backbone and side-chain flexibility.

Main Results:

  • The rigid docking stage achieved medium/acceptable accuracy for 70% of complexes within the top 10 configurations.
  • Considering all configurations, medium/acceptable accuracy reached 94%.
  • Incorporating side-chain and backbone flexibility improved both the best binding conformation and top 10 rankings.

Conclusions:

  • The developed method provides a robust framework for protein-protein docking.
  • Explicitly handling backbone and side-chain flexibility enhances prediction accuracy.
  • The approach is a foundation for future docking methods integrating multiple flexible motions.