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Evaluating ligand docking methods for drugging protein-protein interfaces: insights from AlphaFold2 and molecular

Jordi Gómez Borrego1, Marc Torrent Burgas2

  • 1The Systems Biology of Infection Laboratory, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain.

Journal of Cheminformatics
|September 26, 2025
PubMed
Summary

AlphaFold2 models perform comparably to experimental structures in protein-protein interaction docking. Structural refinement can improve outcomes, but scoring functions limit overall docking performance.

Keywords:
AlphaFoldBenchmarkingMolecular dockingMolecular dynamicsProtein interactionVirtual screening

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