TCRBuilder

Prediction Results

Job ID:TCRBuilder_example
Job name:my_example_model
Job status:finished!
Log file:

    TCRBuilder                                             || || 
    Prediction of T-Cell Receptor Structures              |VB|VA| 
    Built by OPIG                                         |CB|CA|
    Authors: Wing Ki Wong, Claire Marks, Jinwoo Leem    -----------
    Industrial Supervisors: Alan P. Lewis, Jiye Shi
    Supervisor: Charlotte M. Deane

    Model abTCRs using template-based approaches.

    Procedure:
        o Select framework templates
            - Find the template with the same IMGT gene
            - If CDR1 and CDR2 have the same length, use these as templates
        o Predict the orientation
            - Use the orientation from a structure with the highest template identity
        o Predict the CDRs
            - Predict in order of CDRB1, CDRA1, CDRB2, CDRA2, CDRB3, CDRA3 using FREAD (Choi, Deane, 2010)
        o Predict the side chains
            - Use a TCR-specific version of the PEARS algorithm (Leem et al., 2018)

*-Starting TCR assembly-*
-------------------------

Job name: my_example_model
>Beta Chain
ADVTQTPRNRITKTGKRIMLECSQTKGHDRMYWYRQDPGLGLRLIYYSFDVKDINKGEISDGYSVSRQAQAKFSLSLESAIPNQTALYFCATSDESYGYTFGSGTRLTVV
>Alpha Chain
AQSVTQLGSHVSVSEGALVLLRCNYSSSVPPYLFWYVQYPNQGLQLLLKYTSAATLVKGINGFEAEFKKSETSFHLTKPSAHMSDAAEYFCAVSEQDDKIIFGKGTRLHILP
-------------------------

Using ANARCI to annotate the target sequence.
TCRb variable domain identified.
Species identified as human
ADVTQTPRNRITKTGKRIMLECSQTKGHDRMYWYRQDPGLGLRLIYYSFDVKDINKGEISDGYSVSRQAQAKFSLSLESAIPNQTALYFCATSDESYGYTFGSGTRLTVV
*************************************************************************************************************-
Trimming beta sequence to the variable domain (*) only.

TCRa variable domain identified.
Species identified as human
AQSVTQLGSHVSVSEGALVLLRCNYSSSVPPYLFWYVQYPNQGLQLLLKYTSAATLVKGINGFEAEFKKSETSFHLTKPSAHMSDAAEYFCAVSEQDDKIIFGKGTRLHILP
***************************************************************************************************************-
Trimming alpha sequence to the variable domain (*) only.


Writing the ANARCI annotation to file
Done. See my_example_model/alignments/target_numbering.txt

Choosing framework templates
Chose 4x6b chain B with sequence identity over beta chain framework of 0.65
Chose 6eh8 chain A with sequence identity over alpha chain framework of 0.97

Predicting the orientation
Using the angles BA=-51.57, dc=16.33, AC2=78.78, AC1=122.45, BC1=77.72, BC2=105.34 inherited from structure 6fr9_B_A_0 with Fv sequence identity 1.00
Assembling the framework template

Using TRangle to orientate the template chains


Starting CDR prediction procedure.
Running CDR-specific FREAD on CDRB1
1 hits found 
Running CDR-specific FREAD on CDRA1
1 hits found 
Running CDR-specific FREAD on CDRB2
1 hits found 
Running CDR-specific FREAD on CDRA2
3 hits found 
Running CDR-specific FREAD on CDRB3
0 hits found 
0 hits found 
0 hits found 
Running CDR-specific FREAD on CDRA3
1 hits found 
1 hits found 
1 hits found 

FREAD did not find a decoy for the following model(s): fread_prediction_1, fread_prediction_2, fread_prediction_0

Using BLOSUM to find CDRB3 template for fread_prediction_0.
Picked CDRB3 from 5jziE with BLOSUM62 score 1.
This template is the same length loop as the sequence (10 residues)

Using BLOSUM to find CDRB3 template for fread_prediction_1.
Picked CDRB3 from 5jziE with BLOSUM62 score 1.
This template is the same length loop as the sequence (10 residues)

Using BLOSUM to find CDRB3 template for fread_prediction_2.
Picked CDRB3 from 5jziE with BLOSUM62 score 1.
This template is the same length loop as the sequence (10 residues)

Predicting side chains with PEARS

Predicting side chains with PEARS

Predicting side chains with PEARS

Writing modelling report



*--End of TCR assembly--*

Exiting with success code.

Downloads
Model structures(PDB format):
Model 1 Download
Model 2 Download
Model 3 Download
Log file: Download
ANARCI sequence numbering: Download
Zip file containing all output from modelling job: Download


Template Details
Target/Template Sequence Alignment

Alpha chain target-templates alignment

Beta chain target-templates alignment


Match Mismatch Gap CDR
Target/Template Sequence Alignment

Alpha chain target-templates alignment

Beta chain target-templates alignment


Match Mismatch Gap CDR
Target/Template Sequence Alignment

Alpha chain target-templates alignment

Beta chain target-templates alignment


Match Mismatch Gap CDR