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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-Drug Binding: Determination Methods01:22

Protein-Drug Binding: Determination Methods

Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...
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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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 benchmark version 4.0.

Howook Hwang1, Thom Vreven, Joël Janin

  • 1Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

Proteins
|September 1, 2010
PubMed
Summary
This summary is machine-generated.

The protein-protein docking benchmark was updated to version 4.0, adding 52 new complexes for a total of 176 cases. This updated benchmark aids in developing and assessing protein-protein docking methods.

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Last Updated: Jun 9, 2026

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

Background:

  • Protein-protein interactions are crucial for cellular functions.
  • Accurate prediction of protein complex structures is essential for understanding biological processes.
  • Existing protein-protein docking benchmarks require regular updates to include newly resolved structures.

Purpose of the Study:

  • To update the protein-protein docking benchmark with recently available high-resolution complex structures.
  • To provide an expanded dataset for the development and evaluation of protein-protein docking algorithms.
  • To assess the difficulty of newly added cases for docking methods.

Main Methods:

  • Inclusion of 52 new high-resolution protein complex structures into the existing benchmark.
  • Selection of nonredundant complexes at the family-family pair level.
  • Ensuring availability of X-ray or NMR unbound structures for constituent proteins.

Main Results:

  • Benchmark 4.0 now contains 176 unbound-unbound cases, a 42% increase from Benchmark 3.0.
  • Seventeen new enzyme-inhibitor complexes were added; no new antigen-antibody complexes were included.
  • Newly added cases were classified by docking difficulty: 33 rigid body, 11 medium, and 8 difficult.

Conclusions:

  • Benchmark 4.0 offers a significantly expanded and updated resource for protein-protein docking research.
  • The new dataset facilitates rigorous assessment of docking algorithm performance.
  • Public accessibility of Benchmark 4.0 promotes reproducible research and method development.