To use TCRpMHCmodels you will need the license key for the modeling program MODELLER. To get the MODELLER license key you need to fill out the MODELLER License Agreement at http://salilab.org/modeller/registration.html.
TCRpMHCmodels predicts the three-dimensional structure of TCR-pMHC class I complexes using comparative modelling. Upon submission, this tool automatically selects the best templates and provides within minutes a complete three-dimensional model.
The input must include all protein chains from the TCR-pMHC complex (the TCR alpha chain, the TCR beta chain, the peptide chain and the MHC chain), separated by a fasta header. The tool will automatically detect the chain types.
Click on the "Submit" button. The status of your job (either 'queued' or 'running') will be displayed and constantly updated until it terminates and the server output appears in the browser window. At any time during the wait you may enter your e-mail address and simply leave the window. Your job will continue; you will be notified by e-mail when it has terminated. The e-mail message will contain the URL under which the results are stored; they will remain on the server for 24 hours for you to collect them.
After the server successfully finishes the job, a summary page shows up. Use the "Download" button to download the generated PDB file.