AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
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Updated: Jun 23, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
Garrett M Morris1, Ruth Huey, William Lindstrom
1Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
Abstract:
We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redocking experiment with 188 diverse ligand-protein complexes and a cross-docking experiment using flexible sidechains in 87 HIV protease complexes. We also report its utility in analysis of covalently bound ligands, using both a grid-based docking method and a modification of the flexible sidechain technique.
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