MODELLER not detected. Defaulting to using Sphinx if necessary
ABodyBuilder \\ //
An Antibody Modelling Protocol \\ //
Built by OPIG ||
Authors: Jinwoo Leem & James Dunbar. ||
Supervisor: Charlotte Deane
ABodyBuilder uses:
o ANARCI to annotate the antibody sequence.
o SAbDab to select templates for the framework regions.
o ABangle to predict the VH-VL orientation.
o FREAD to model the CDR regions.
o PEARS to build side chains
o Sphinx or MODELLER to model loops
if an ab-intio method is required
o MODELLER to model insertions in
the framework region if necessary.
Input parameters:
Job name = my_example_model
Job ID = my_example_model
Heavy sequence = VKLLEQSGAEVKKPGASVKVSCKASGYSFTSYGLHWVRQAPGQRLEWMGWISAGTGNTKYSQKFRGRVTFTRDTSATTAYMGLSSLRPEDTAVYYCARDPYGGGKSEFDYWGQGTLVTVSS
Light sequence = ELVMTQSPSSLSASVGDRVNIACRASQGISSALAWYQQKPGKAPRLLIYDASNLESGVPSRFSGSGSGTDFTLTISSLQPEDFAIYYCQQFNSYPLTFGGGTKVEIKRTV
Produce 1 models
Started modelling
Using anarci to annotate the target sequences
Heavy variable domain identified in heavy sequence
Species identified as human
VKLLEQSGAEVKKPGASVKVSCKASGYSFTSYGLHWVRQAPGQRLEWMGWISAGTGNTKYSQKFRGRVTFTRDTSATTAYMGLSSLRPEDTAVYYCARDPYGGGKSEFDYWGQGTLVTVSS
*************************************************************************************************************************
Trimming heavy sequence to the variable domain (*) only.
Kappa variable domain identified in light sequence
Species identified as human
ELVMTQSPSSLSASVGDRVNIACRASQGISSALAWYQQKPGKAPRLLIYDASNLESGVPSRFSGSGSGTDFTLTISSLQPEDFAIYYCQQFNSYPLTFGGGTKVEIKRTV
***********************************************************************************************************---
Trimming light 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 1vge chain H with sequence identity over heavy chain framework of 1.00
Chose 1vge chain L with sequence identity over light chain framework of 1.00
Using 1vge H L as the orientation template
Using the angles HC2=114.93, HC1=72.89, LC2=83.20, LC1=118.83, dc=16.19, HL=-59.72 inherited from structure 1vge_H_L_0 with sequence identity 1.00
Assembling the framework template
Using ABangle to orientate the template chains
Starting CDR prediction procedure.
FREAD cdr protocol started.
Running CDR-specific FREAD on CDR L2
>10 hits found
Running CDR-specific FREAD on CDR H2
>10 hits found
Running CDR-specific FREAD on CDR L1
>10 hits found
Running CDR-specific FREAD on CDR H1
>10 hits found
Running CDR-specific FREAD on CDR L3
>10 hits found
Running CDR-specific FREAD on CDR H3
>10 hits found
Predicting side chains with PEARS
Detecting and building disulphide bridges first, as necessary...
Detecting and building unimodal rotamers...
Building remaining rotamers...
Precomputing energies of possible rotamers...
Running DEE...
Building an interaction graph...
Detecting and searching biconnected components...
Solving remaining clusters...
Filling in remaining gaps...
Writing modelling report
Renumbering model files with the imgt numbering scheme
Finished modelling
Exiting with success code.