Figure 3.

The multi-stage TCR/pMHC docking protocol, TCRFlexDock. After the unbound TCR and pMHC oriented to a starting position, the CDR3 loops are perturbed and minimized, and a coarse-grained centroid docking search is followed by two iterations of CDR (and optionally peptide) loop refinement and 6D rigid body movements plus side chain repacking. This is repeated 1000 times, resulting in 1000 predictions per test case, which are then scored using ZRANK to select docking models. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]