Challenges in protein docking
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Updated: Dec 11, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
1Computational Biology Program and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA.
Abstract:
Current developments in protein docking aim at improvement of applicability, accuracy and utility of modeling macromolecular complexes. The challenges include the need for greater emphasis on protein docking to molecules of different types, proper accounting for conformational flexibility upon binding, new promising methodologies based on residue co-evolution and deep learning, affinity prediction, and further development of fully automated docking servers. Importantly, new developments increasingly focus on realistic modeling of protein interactions in vivo, including crowded environment inside a cell, which involves multiple transient encounters, and propagating the system in time. This opinion paper offers the author's perspective on these challenges in structural modeling of protein interactions and the future of protein docking.
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