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Related Concept Videos

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...
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...
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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 13, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

The HADDOCK web server for data-driven biomolecular docking.

Sjoerd J de Vries1, Marc van Dijk, Alexandre M J J Bonvin

  • 1Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, Utrecht, The Netherlands.

Nature Protocols
|May 1, 2010
PubMed
Summary
This summary is machine-generated.

The HADDOCK web server simplifies biomolecular complex modeling using computational docking. This user-friendly tool supports diverse experimental data for accurate structure prediction.

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Last Updated: Jun 13, 2026

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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Published on: July 8, 2025

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

Published on: June 20, 2025

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Molecular modeling

Background:

  • Computational docking predicts 3D structures of biomolecular complexes from individual molecular structures.
  • HADDOCK is a widely used docking program employing a data-driven strategy and supporting extensive experimental data.
  • Modeling biomolecular complexes is crucial for understanding biological processes and drug discovery.

Purpose of the Study:

  • To present the HADDOCK web server protocol for accessible biomolecular complex modeling.
  • To provide a user-friendly interface for basic docking tasks.
  • To offer advanced options for users leveraging comprehensive experimental data and customized docking.

Main Methods:

  • Utilizing the HADDOCK program via a web server interface.
  • Inputting individual component structures and lists of interacting residues for basic modeling.
  • Employing additional web interfaces for advanced users to integrate diverse experimental data and customize docking parameters.
  • Leveraging dedicated cluster resources and the e-NMR GRID infrastructure for computational power.

Main Results:

  • A user-friendly web interface for computational docking has been established.
  • The server facilitates the modeling of biomolecular complexes for a broad scientific community.
  • Advanced options allow for the integration of a wide range of experimental data.
  • Docking runs are efficient, with preparation taking minutes and completion in hours.

Conclusions:

  • The HADDOCK web server protocol democratizes biomolecular complex modeling.
  • It offers a scalable and efficient platform for structural bioinformatics research.
  • The combination of user-friendliness and advanced capabilities makes HADDOCK a valuable tool for diverse research needs.