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What is the scoring cutoff for "good-scoring states" in VSW? What do the "All states", "All good scoring states", and "Only best scoring state" options mean?

The scoring cutoff is the GlideScore that retains the desired number, or percent, of compounds.

The post-processing of the Glide docking stage reduces the results to the desired number or percentage of compounds to keep. It can either save just the top pose per compound (best by title), or all poses (going up in score) until the desired number/percent of compounds is saved. So the worst-scoring compound will have one pose (and therefore a single variant/state), while better scoring compounds could have multiple poses/states. The PULL stage then retrieves the original geometries for the next docking stage; it goes through the docking output and gets matching structures from the original ligand set. This matching can be done by compound or state identifier. If the matching is by state, only the docked and kept state will be passed on to the next stage. If the matching is by compound, all states of a docked and kept compound will be passed on to the next stage. So the meanings of the three options are:

Only best scoring state: The Glide post-processing saves best-by-title (i.e., one state and pose per compound), and then structures are pulled from the original ligand set by state identifier.

All good scoring states: The Glide post-processing saves all poses/states until the last desired compound is kept, and then structures are pulled from the original ligand set by state identifier.

All states: The Glide post-processing saves all poses/states until the last desired compound is kept, and then structures are pulled from the original ligand set by compound identifier (grabbing all states of each kept compound).

The interplay of the Glide post-processing and the PULL stages makes these options difficult to understand. Please note that the last docking stage (usually XP) won't have an "All states" option, because all states of a compound can be retrieved only if there is a subsequent PULL stage, which make sense only if there is another docking stage.

Keywords: VSW, states, compounds, docking, keep

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