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

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Published on: June 20, 2025

Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server.

Ezgi Karaca¹, Adrien S J Melquiond, Sjoerd J de Vries

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

Molecular & Cellular Proteomics : MCP

|March 23, 2010

Summary

This summary is machine-generated.

High Ambiguity-Driven Docking (HADDOCK) offers a new web interface for modeling large biomolecular assemblies. This tool effectively predicts structures of complexes using experimental or bioinformatics data, crucial for understanding biological networks.

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Last Updated: Jun 14, 2026

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

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Published on: June 20, 2025

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

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

Area of Science:

Structural biology
Computational biology
Biophysics

Background:

Large-scale proteomics studies yield extensive interactome data.
Classical experimental methods face challenges in determining the 3D structures of these complexes.
Computational modeling, particularly docking, is essential for elucidating complex structures.

Purpose of the Study:

To introduce a novel web interface for the High Ambiguity-Driven Docking (HADDOCK) program.
To enable simultaneous docking of up to six biomolecules, including symmetric assemblies.
To integrate diverse experimental and bioinformatics data for enhanced modeling accuracy.

Main Methods:

Development of a user-friendly web interface for HADDOCK.
Implementation of support for docking multiple molecules (up to six) with various symmetry types.
Testing the server on benchmark cases of symmetric protein and protein-DNA complexes.

Main Results:

The HADDOCK web server successfully modeled symmetric multicomponent assemblies.
In all tested cases, HADDOCK generated high-quality structural solutions when driven by data.
The tool ranked the correct models at the top, demonstrating its predictive power.

Conclusions:

HADDOCK's enhanced web interface is effective for modeling symmetric macromolecular assemblies.
Integrating experimental or bioinformatics data significantly improves docking accuracy.
Docking methods are vital for adding structural information to interactomes, with experimental data remaining highly desirable for complex systems.