Short Trajectory MD with Analysis
The Floe Short Trajectory MD with Analysis (STMD) is for pose validation. You should start with a ligand with one or more conformers already well-posed in the active site, with protein-ligand interactions in place, serving as hypotheses for ligand binding. Each pose will be evaluated by this Floe to be validated (or not) as a good pose. We are not primarily asking the question “what is the pose for this ligand?” but rather “is this a good pose for this ligand?”, or with multiple poses, “which of these poses is best?” We seek an answer by running a short MD trajectory on each pose separately and comparing the results to the starting (input) pose and between the poses (if more than one).
In addition to the equilibrium simulations on the ligand-bound states for pose validation, the Floe also runs equilibrium simulations on the ligand-unbound states so that the output ligand-bound/unbound datasets of the Floe can be directly used in nonequilibrium switching (NES) Flows without the need for additional equilibrium simulations after STMD for pose validation.