Enhanced Sampling Molecular Dynamics

Dynamic Docking

Most interesting molecular 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:

 

1) an unbinding protocol that ranks congeneric ligands based on their residence time in a given target binding site;

 

2) a technique to perform fully flexible protein ligand dynamic docking;

 

3) a tool to dynamically characterize water persistency and “happiness” in binding sites.