TCRmodel server can be used to model the unbound TCR structure and TCR structure in complex with peptide-MHC structures. Both Class I and Class II MHC complexes are supported. The main server page has two sections:
- TCR-pMHC complex modeling
- Unbound TCR modeling
Input forms: TCR-pMHC complex modeling
The users can provide the input for the TCR-pMHC complex modeling in two ways:
- Enter the sequence in the text box
- Select the germline gene from dropdown menu
Input forms: Unbound TCR modeling
TCR sequences for modeling can be submitted as amino acid sequences for alpha and beta chains, encompassing at minimum the TCR variable domains. The TCRmodel server will automatically identify germline genes in the input sequences, if there is an exact match in the database.
Alternatively, users can specify germline gene and CDR3 loop sequences, and generate the full TCR variable domain sequences using the "Generate TCR Sequences" button.
Users can optionally exclude closely related structures as templates for modeling (for benchmarking), and can optionally have Rosetta perform refinement of modeled CDR3 loops through kinematic closure sampling. These additional refinement steps generally improve modeling performance when related CDR3 templates are not available, but will increase processing time. By default, grafted and relaxed TCR models are returned within one minute.
Output model & viewer
After submission of TCR sequences, the results page will provide the parsed CDR loop sequences and identified templates to the user. When modeling completes, the results page will be automatically updated. The result page includes an interactive viewer showing the modeled TCR structure, downloadable model coordinates, and the model amino acid sequence. The completed results page also includes three different sections: Template information, Sequence alignment and TCR segments.
The templates used for the modeling are provided for all the TCR segments with corresponding PDB and chain id's.
Sequence alignments between model and template TCR structures are provided for all the CDR loop sequences.
Parsed TCR segments
The parsed sequence segments of input TCR sequences are provided in this section. This includes the variable domains, framework segments, CDR1, CDr2, CDR3 loop sequences for both TCR α and β chains.