The HADDOCK2.4 web server for integrative modeling of biomolecular complexes

Area of Science:

• Structural biology
• Computational biology
• Biophysics

Background:

• Macromolecular interactions are vital for cellular processes.
• Experimental methods face limitations in resolving large, heterogeneous complexes at atomic resolution.
• Integrative computational approaches complement experimental data in structural biology.

Purpose of the Study:

• Introduce HADDOCK2.4, an updated integrative modeling platform and web interface.
• Facilitate the generation of high-quality models for macromolecular complexes.
• Enhance user experience through automated features and distributed computing.

Main Methods:

• Integrative modeling combining diverse experimental and theoretical data.
• Utilizing HADDOCK2.4 web server with automated parameter settings and pre/post-processing.
• Demonstrating applications in antibody-antigen complex structure prediction and coarse-grained modeling of PRC1-nucleosome interactions.

Main Results:

• Successful prediction of antibody-antigen complex structure using NMR and antibody knowledge.
• Coarse-grained modeling of PRC1 with a nucleosome guided by mutagenesis and functional data.
• Demonstrated HADDOCK2.4's capability to model diverse macromolecular assemblies.

Conclusions:

• HADDOCK2.4 provides a user-friendly platform for modeling complex biomolecular assemblies.
• The updated web server supports structural biologists and non-experts in exploring intricate structures.
• Integrative modeling with HADDOCK2.4 advances the understanding of cellular functions through structural insights.