Most interesting m             olecular phenomena often occur on a timescale which is out of reach for   conventional "brute force" Molecular Dynamics (MD) simulation. Enhanced Sampling techniques act so as to achieve a statistically significant sampling of relevant regions of the conformational space. This can be done in several way, such as by adding ad hoc external potentials or by tweaking some parameters of the simulation itself. In the natural search of a trade-off between speed and accuracy, here below are presented a few approaches which aim at extracting from MD simulation useful information with reasonable computational effort:

• an unbinding protocol that ranks congeneric ligands based on their residence time in a given target binding site;
• a technique to perform fully flexible protein ligand dynamic docking;
• a tool to dynamically characterize water persistency and “happiness” in binding sites.

Ongoing projects:

 

CLC proteins - chloride channels and transporters

 

Using combined computational and experimental approach we investigate the effects of mutations on the function of proteins affected in rare genetic diseases. Within the project, our group is involved in enhanced sampling MD simulations and software development.

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Project funding: