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Updated: Mar 24, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
Adaptive BP-Dock: An Induced Fit Docking Approach for Full Receptor Flexibility
1Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, United States.
Adaptive BP-Dock improves drug discovery by simulating protein and ligand changes during docking. This flexible approach enhances accuracy for identifying novel drug targets.
Area of Science:
- Computational biology
- Structural biology
- Drug discovery
Background:
- Induced fit effects are crucial for accurate molecular docking.
- Traditional docking methods often struggle with protein conformational flexibility.
- Efficiently modeling protein-ligand interactions is key for rational drug design.
Purpose of the Study:
- To develop an adaptive induced fit docking approach.
- To integrate perturbation response scanning (PRS) with RosettaLigand.
- To improve the accuracy and efficiency of molecular docking for drug discovery.
Main Methods:
- Developed Adaptive BP-Dock, integrating PRS with RosettaLigand.
- Perturbed receptor binding pocket residues to obtain new conformations via PRS.
- Iteratively docked ligands to updated receptor conformations.
Main Results:
- Adaptive BP-Dock showed better correlation with experimental binding affinities than other protocols.
- Successfully tested on challenging unbound docking cases (e.g., HIV-1 reverse transcriptase, HIV-1 protease).
- Demonstrated ability to capture binding-induced conformational changes.
Conclusions:
- Adaptive BP-Dock effectively models simultaneous protein and ligand conformational changes.
- Offers a faster and more efficient docking method for novel targets.
- Enhances rational drug design by improving the prediction of binding interactions.
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