To see a demonstration of using the modelling server, check out our video!
To create a model of your antibody:
- Go to the Antibody Modelling page.
- Submit the amino-acid sequences of your desired antibody (heavy and light chains). This can be done by copying and pasting the amino-acid sequence for each chain into the corresponding text-box.
- Name your model in the "Job Name" box (only alphanumeric characters, spaces and the characters +_.- can be used).
- [Optional] Choose which numbering scheme should be used to annotate the final model structure(s). The Kabat, Chothia, Martin (Enhanced Chothia) and IMGT numbering schemes are available.
- Click on the "Model" button to start.
The modelling process is fully automated. When you click "Model", the following steps will be performed:
- The heavy and light sequences are initially numbered using the IMGT numbering scheme via ANARCI
- The North/AHo definition of CDR loops and framework regions is used throughout.
- Templates for the VH and VL domain framework are chosen from SAbDab based on sequence identity.
- The VH-VL orientation is chosen using ABangle and the VH and VL templates are orientated in the chosen pose
- CDR loops are modelled using CDR-specific FREAD. If no acceptable template is found, then a second round of searching is performed on antibody-specific FREAD. If this still does not yield a suitable template, this is noted and a separate template is chosen based on sequence similarity and length. If necessary, MODELLER is used to model loops ab-initio.
- Once assembled, PEARS is used to predict the side chains.
- The final model is analysed and renumbered with the chosen scheme. A modelling report is generated that estimates how accurate each region is given the choices made, methods used and scores calculated when building your model.
On submission, you will be taken to a modelling results page. From here you can check the status of your job and view snapshots of the log file. Multiple jobs can be monitored from the Jobs page
An example output can be seen here. Output for Modelling consists of:
- Summary Information
- The log file detailing the decisions made through the modelling process
- A sequence annotation file giving the numbering of your submitted sequence
- An archive zip file containing all the models, templates and modelling details for the job.
- Models. The model ranked "1" is considered the best.
- The model file contains the coordinates in PDB format.
- The View Model Annotations link takes you to the model annotation page (see below).
- Template details
- A table listing the template region, the template structure, the selection method and the score. For FREAD results, the score is the environment specific substitution score. Otherwise the score is the sequence identity over the region.
- An alignment between your submitted target sequence and the templates chosen. Use the selection at the bottom to change the definition of CDR (highlighted in red).
The results page allows you to annotate your model with structure and sequence based properties or to use it in SAbPred's paratope
prediction applications. To do so click on the corresponding option in the 'Action' drop-down menu next to the model details.
Once an Fv model has been predicted it is annotated with a range of properties [Example].
- All numbering shown will be in the scheme you chose at the input page (Chothia, Kabat, IMGT [used in ABodyBuilder] or Martin/Enhanced Chothia).
- A bio-PV visualisation of your model will be shown (we strongly recommend using Google Chrome to load this page). Click the buttons on the right hand side to change which type of annotation is shown, and the buttons on the left to change how the structure is represented. The available annotations are as follows:
- Secondary structure. The molecule is annotated as either alpha helix, beta strand, beta turn or loop.
- Domain and CDR definition. VH and VL domains are coloured green and cyan respectively. CDRs are coloured red. The CDR definition used can be either Kabat, Chothia, IMGT, Aho/North (this is used in ABodyBuilder) or Contact.
- Solvent exposure. DSSP is used to calculate the accessible surface area. This value is scaled by the standard accessibilities to give the relative exposure. Residues that are less than 10% exposed are considered buried.
- Estimated accuracy. Each of the choices that can be made in the modelling procedure has been benchmarked. We use this information to estimate how well each region of the model is likely to have been predicted. For example, 75% of VH framework structures with sequence identity of 80% +/- 2.5% have a backbone RMSD of 1Å or better. Therefore if the model has been predicted using a template with 80% sequence identity to the target we have a confidence of 75% that the VH framework is modelled to within 1Å RMSD. Use the sliders to change the thresholds.
- Sequence liabilities. Sequence motifs that are known to cause issues for antibody development are mapped onto the structure. Use the buttons to toggle them on and off. Click the checkbox to hide those that are not exposed to the solvent.
For a full description of the method or if you use this software, please refer to:
Leem et al.
ABodyBuilder: automated antibody structure prediction with data-driven accuracy estimation. mAbs (2016)