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TCR-CoM

For questions about running the script or for reporting bugs, please contact:

Brian Baker(brian-baker[at]nd.edu)
or
Esam Abualrous(e.abualrous[at]fu-berlin.de)

Description

Calculates the geometrical parameters (r, theta, phi) of T cell receptors (TCR) on the top of MHC proteins

Citation

If you find this tool useful, please cite:

Singh, NK, Abualrous, ET, Ayres, CM, et al. Geometrical characterization of T cell receptor binding modes reveals class‐specific binding to maximize access to antigen. Proteins. 2019; 1– 11. https://doi.org/10.1002/prot.25829

Python script

USAGE

1- For peptide-MHC class I-TCR complex:

python tcr_com_ref-dep_v5.py -pdbid XXX -mhc_chain_a A -tcr_chain_a D -tcr_chain_b E -output_pdb True

2- For peptide-MHC class II-TCR complex:

python tcr_com_ref-dep_v5.py -pdbid XXX -mhc_chain_a A -mhc_chain_b A -tcr_chain_a D -tcr_chain_b E -output_pdb True

Pymol plugin

USAGE

1- For peptide-MHC class I-TCR complex:

tcr_mhci_pos selection [,mhc_a=None [,tcr_a = None [,tcr_b = None [,mhc_a_init=1 [,mhc_a_final=180 [,tcr_a_init=1 [,tcr_a_final=109 [, tcr_b_init=1 [,tcr_b_final=116 [,state=None ]]]]]]]]]]

2- For peptide-MHC class II-TCR complex:

tcr_mhcii_pos selection [,mhc_a=None [,mhc_b=None [,tcr_a = None [,tcr_b = None [,mhc_a_init=1 [,mhc_a_final=80 [,mhc_b_init=1 [,mhc_b_final=90 [,tcr_a_init=1 [,tcr_a_final=109 [, tcr_b_init=1 [,tcr_b_final=116 [,state=None ]]]]]]]]]]]]]

Notes

  • The approach is available as Python code, Pymol plugin, and online tool: https://tcr3d.ibbr.umd.edu/tcr_com
  • The submitted PDB-file should be refined by one of the available PDB-editors to avoid inaccurate results
  • Due to differences in implementation, small differences may be observed between the output values of the Python code and the Pymol plugin.
  • The code requires defining at least three chain-IDs for MHCI-TCR or four chain-IDs for MHCII-TCR
  • Please make sure that the defined chains do not contain any non-protein atoms