The plausible association sites in the aforementioned description of TTPSite® are employed in TTPDock The TTProbes® are individually computationally docked and scored, using sophisticated software modules, across the ensemble of association sites in each 3D model.   This docking and scoring routine is computationally intense; however, the operation is easily parallelized across a multi-node computing cluster.

One or more scoring functions may be used to rank the fit of any TTProbe® in each association site.   Frequently a consensus score is used, with each association site (selected from TTPSite®) linked to a docking score for each TTProbe® in that association site.  This data is very useful in the ensuing modules, TTPSelect® and TTPScreen®.