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Published on Dec 18, 2014
Scalable On-Board Multi-GPU Simulation of Long-Range Molecular Dynamics (2014)
The video shows a drug binding with a sodium-potasium pump and its FYXD10 regulatory protein on a cell membrane. The system is surrounded by water molecules and ions acting as solvent, which are not shown in the video for clarity. The drug works as an inhibitor of the sodium-potasium pump, which is over-activated in certain types of cancer. Knowing the actual binding of the drug allows us to identify key atoms in the binding, and thus improve the design of the molecule.
The position of the drug is initiliazed using molecular docking, and then the system is simulated in normal temperature and pressure conditions. In the first few nanoseconds the binding is unstable because the placement produced through docking is not realistic. After several tens of nanoseconds the drug finds its actual stable binding mode.