Short Trajectory MD with Analysis
The Short Trajectory MD with Analysis (STMD) Floe is used 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 in order to be validated (or not) as a good pose. The primary question is not “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?”). To answer this question, the floe runs a short MD trajectory on each pose separately and compares 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 the FE-NES for Binding Affinity Prediction Floe without the need for additional equilibrium simulations after STMD for pose validation.