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. 2023 May 4;51(W1):W569–W576. doi: 10.1093/nar/gkad356

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© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 3. — Example TCR–pMHC modeling output from TCRmodel2. (A) A TCR–pMHC complex with a human TCR, SARS-CoV-2 nucleocapsid epitope and HLA-B*07:02 MHC from a recent study (39) was modeled using TCRmodel2. The visualization of the top-ranked model from the Results page is shown, with TCR α chain red, β chain orange, peptide cyan and MHC blue. (B) The interface between the TCR and pMHC of the top-ranked model is shown, with TCR, peptide and MHC chains colored as in panel (A), and shared CDR3β motif residues (sequence: PLVGAP) colored green and shown as sticks. Peptide residues are shown as sticks, and TCR CDR1β and CDR2β residues interacting with the MHC and/or peptide are shown as sticks and circled. Structure visualized using PyMOL (Schrödinger, Inc.).