GPCRs: thinking in 3D - MMS

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... thinking in 3D!!

Supervised Molecular Dynamics (SuMD)

Summary:

We have developed a helpful approach to simulate a receptor-ligand recognition pathway based on GPU-driven membrane molecular dynamics simulation in an appreciable short time scale. Combining two very well known and consolidated computational approaches such as molecular dynamics and an a tabu-like algorithm to supervise the evolution of receptor-ligand trajectory, we are able to accurately completely explore the receptor-ligand event in a nanosecond time scale. This approach is also very useful to analyze both orthosteric an allosteric binding events broadening our perspectives in several scientific areas from molecular pharmacology to drug discovery.

Trajectories:

ZM241385-human A2A Adenosine Receptor
T4G-human A
2A Adenosine Receptor

T4E-human A2A Adenosine Receptor

Caffeine-human A2A Adenosine Receptor

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Reference:

Sabbadin D., Moro S. J Chem Inf Model 54, 372-6 (2014)

Cuzzolin A. et al. J Chem Inf Model 56, 687-705 (2016)

 
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