SwarmDock and the Use of Normal Modes in Protein-Protein Docking
Abstract
:1. Introduction
2. Results and Discussion
2.1. Overlap
2.1.1. Rotations-Translation-in-Blocks Method
2.2. Linear Combinations of Normal Modes
2.3. Docking as a Function of Normal Modes
3. Conclusions
4. Experimental Section
4.1. Normal Mode Analysis
4.1.1. The Rotation-Translation-of-Blocks Method
4.1.2. Overlap
4.1.3. Data Set
4.2. Analytical Mapping of Unbound to Bound
4.3. SwarmDock
4.3.1. Search Space
4.3.2. Initialisation
4.3.3. Propagation
4.3.4. Velocity Clamping
4.3.5. Local Minimisation
4.3.6. Clustering
4.3.7. Analysis of Docked poses
4.3.8. Energy Function
Acknowledgements
References
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Complex | Modes: 1–10 | 11–20 | 21–30 | 31–40 |
---|---|---|---|---|
1AY7 | 15.1 | 11.2 | 12.3 | 14.3 |
1GCQ | 1.2 | 1.9 | 2.9 | 2.6 |
1E6J | 10.0 | 9.9 | 11.0 | 11.5 |
1TMQ | 2.1 | 2.9 | 4.7 | 2.9 |
1EER | 3.6 | 3.1 | 5.3 | 5.9 |
1K5D | 5.9 | 6.9 | 7.4 | 6.6 |
1GRN | 26.6 | 28.7 | 29.3 | 27.3 |
1KKL | 2.8 | 2.9 | 3.9 | 5.6 |
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Moal, I.H.; Bates, P.A. SwarmDock and the Use of Normal Modes in Protein-Protein Docking. Int. J. Mol. Sci. 2010, 11, 3623-3648. https://doi.org/10.3390/ijms11103623
Moal IH, Bates PA. SwarmDock and the Use of Normal Modes in Protein-Protein Docking. International Journal of Molecular Sciences. 2010; 11(10):3623-3648. https://doi.org/10.3390/ijms11103623
Chicago/Turabian StyleMoal, Iain H., and Paul A. Bates. 2010. "SwarmDock and the Use of Normal Modes in Protein-Protein Docking" International Journal of Molecular Sciences 11, no. 10: 3623-3648. https://doi.org/10.3390/ijms11103623