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Updated: Nov 24, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Advances to tackle backbone flexibility in protein docking.

Ameya Harmalkar¹, Jeffrey J Gray²

¹Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.

Current Opinion in Structural Biology

|December 28, 2020

Summary

Protein-protein docking struggles with backbone flexibility, hindering accurate complex structure prediction. Recent advances in molecular dynamics, internal coordinates, and machine learning offer new solutions for modeling these dynamic interactions.

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Last Updated: Nov 24, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

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Published on: June 20, 2025

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

Computational biology
Structural bioinformatics

Background:

Protein-protein docking methods predict complex structures but are limited by protein backbone flexibility.
Accurate predictions are achieved in less than 20% of difficult cases involving significant conformational changes.

Purpose of the Study:

To describe recent developments in protein-protein docking.
To highlight advances addressing backbone flexibility in complex formation.

Main Methods:

Enhanced sampling techniques in molecular dynamics and Monte Carlo simulations.
Internal coordinate formulations with harmonic dynamics for monomer and complex motion.
Machine learning approaches, including deep neural networks, for guiding docking and predicting binding sites.

Main Results:

Reduced time-scale limitations in simulations.
Capture of realistic motions in monomers and complexes.
Adaptive guidance of docking and novel binding site predictions.

Conclusions:

Recent computational tools show promise in overcoming the challenge of predicting protein complex structures with significant conformational changes.
Advances in modeling backbone flexibility are crucial for accurate protein-protein docking.