Skip to main content

Table 4 Prediction rates of the test evaluations

From: DynaDom: structure-based prediction of T cell receptor inter-domain and T cell receptor-peptide-MHC (class I) association angles

ESa MHC initial MHC CR d
  orientationb translationc # %
T1 crystal no 53 100.0
T2 crystal yes 38 71.7
T3 general yes 31 58.5
  1. For each test the Q-flip correction as well as the use of distance restraint are systematically applied. The TCR Vβ domain is placed in its original crystal structure orientation and is optimized. The tests are performed for each of the 53 structures present in the DSC data set and the MHC rigid body position is optimized in each case
  2. aEvaluation setting label
  3. bThe initial orientation of the MHC unit is chosen either according to the original crystal structure or using the general zero orientation as for the standard version of our pipeline (see Methods Section for more details)
  4. cInitial translation of the MHC unit to avoid steric hindrance, necessary if the MHC rigid body is not placed according to the crystal structure orientation (see Methods Section for more details)
  5. dAbsolute and relative prediction rate according to the RMSD based criterion (i.e., CR) in data set DSC (53 structures). For each prediction run, a success is counted if the resulting model has an RMSD value lower than 2 Å with respect to the crystal structure