Antigen-antibody interactions play an important role in protecting our body from foreign molecules. This is applied in vaccine development against a disease. In this article, we are going to mention a simple methodology used in studying/ identifying interactions between antigen-antibody complex.

The basic methodology includes:

1. Structure prediction of antigen
2. Structure prediction of antibody
3. Docking of antigen-antibody
4. Analysis
5. Molecular Dynamics (MD) Simulation

1. Structure prediction of antigen

Predict a 3D structure of your antigen of interest using some software such as:

• IEDB Analysis (http://tools.iedb.org/main/bcell/)
• LYRA (http://tools.iedb.org/lyra/)

2. Structure Prediction of antibody

Predict a 3D structure of the antibody using some software such as:

• RosettaAntibody3 (https://www.rosettacommons.org/docs/latest/application_documentation/antibody/antibody-protocol)
• RosettaAntibodyDesign (RAbD) (https://new.rosettacommons.org/docs/latest/application_documentation/antibody/RosettaAntibodyDesign)
• SaBPred (http://opig.stats.ox.ac.uk/webapps/newsabdab/sabpred/)

3. Docking of antigen-antibody

Now, since you have the structures of antigen and antibody, you can go for their docking. For docking of antigen-antibody complex, you can use:

• HADDOCK2.4 web server (https://wenmr.science.uu.nl/haddock2.4/)
• Cluspro2.0 (https://cluspro.bu.edu/login.php)
• ZDOCK (https://zdock.umassmed.edu/)
• LightDock (https://lightdock.org/)

Amongst the above-mentioned tools, HADDOCK provides the best results with high-accuracy models [1].

4. Analysis

For analysis of docking results, you can use software such as Pymol, Discovery Studio Visualizer, Chimera, and so on. Some web servers such as HADDOCK provide a script that you can run in software like Pymol to directly visualize the antigen-antibody interactions.

5. MD Simulation

After successful docking, you should go for an MD simulation of the antigen-antibody complex. It will help you to analyze the stability of the complex. Set an appropriate timescale and other parameters for MD run.

---

This is a basic methodology explained in this tutorial. You can always go for advanced docking considering all parameters including homology modeling or ab initio prediction of antigen and antibody structures.

---

References

1. Ambrosetti, F., Jiménez-García, B., Roel-Touris, J., & Bonvin, A. M. (2020). Modeling antibody-antigen complexes by information-driven docking. Structure, 28(1), 119-129.