This dataset contains 172 100ns pMHC Molecular Dynamics simulation trajectories of Knapp et al. 2015. in review.

The trajectories were converted in the following way:
- Periodic boundary condition artefacts were removed with the options “whole”, “cluster”, and “no jump”.
- The pMHC complexes were centred in the box.
- The pMHC complexes were superimposed rotationally and transnationally onto the first frame of each simulation.
- Each trajectory contains 800 equally distributed simulation frames.
- Water molecules were removed.


When using these data please acknowledge the source and use the following cites:

1) pMHC simulations:
B. Knapp, C. M. Deane. (2015) T-cell receptor binding effects the dynamics of the peptide/MHCI complex. in review.

2) TCRpMHC simulations:
B. Knapp, J. Dunbar, C. M. Deane (2014) Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study. PLoS Comput Biol 10[8], e1003748.