One of the problems we have been very interested in over the years is the problem of ligand binding mode sampling, partly because we find that docking is good at generating plausible ligand binding modes that are stable for relatively long times in MD simulations, but bad at identifying which of these is best. We often then begin MD studies by clustering dock poses, taking members from many different clusters, and then running short MD simulations to identify which are stable. [More…] “Binding mode sampling: What didn’t work (that well)”