A Self-Adaptive Steered Molecular Dynamics Method Based on Minimization of Stretching Force Reveals the Binding Affinity of Protein–Ligand Complexes
Abstract
:1. Introduction
2. Models and Methods
2.1. The Self-Adaptive SMD Strategy
2.2. The Multi-Population Genetic Algorithm
2.3. Choice of Receptor–Ligand Complexes
3. Results and Discussion
3.1. The Influence of the Cut-Off Force
3.2. The Influence of the Pulling Rate
3.3. The Optimized Unbinding Process
3.4. The Relationship of the Rupture Force and Binding Free Energy
4. Conclusions
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Gu, J.; Li, H.; Wang, X. A Self-Adaptive Steered Molecular Dynamics Method Based on Minimization of Stretching Force Reveals the Binding Affinity of Protein–Ligand Complexes. Molecules 2015, 20, 19236-19251. https://doi.org/10.3390/molecules201019236
Gu J, Li H, Wang X. A Self-Adaptive Steered Molecular Dynamics Method Based on Minimization of Stretching Force Reveals the Binding Affinity of Protein–Ligand Complexes. Molecules. 2015; 20(10):19236-19251. https://doi.org/10.3390/molecules201019236
Chicago/Turabian StyleGu, Junfeng, Hongxia Li, and Xicheng Wang. 2015. "A Self-Adaptive Steered Molecular Dynamics Method Based on Minimization of Stretching Force Reveals the Binding Affinity of Protein–Ligand Complexes" Molecules 20, no. 10: 19236-19251. https://doi.org/10.3390/molecules201019236