A protocol for information-driven antibody-antigen modelling with the HADDOCK2.4 webserver

• Main Authors: Ambrosetti, Francesco, Jandova, Zuzana, Bonvin, Alexandre M. J. J
• Format: Journal Article
• Language: English
• Published: 07-05-2020
• Subjects: Quantitative Biology - Biomolecules
• DOI: 10.48550/arxiv.2005.03283

In the recent years, therapeutic use of antibodies has seen a huge growth,
due to their inherent proprieties and technological advances in the methods
used to study and characterize them. Effective design and engineering of
antibodies for therapeutic purposes are heavily dependent on knowledge of the
structural principles that regulate antibody-antigen interactions. Several
experimental techniques such as X-ray crystallography, cryo-electron
microscopy, NMR or mutagenesis analysis can be applied, but these are usually
expensive and time consuming. Therefore computational approaches like molecular
docking may offer a valuable alternative for the characterisation of
antibody-antigen complexes.
Here we describe a protocol for the prediction of the 3D structure of
antibody-antigen complexes using the integrative modelling platform HADDOCK.
The protocol consists of: 1) The identification of the antibody residues
belonging to the hyper variable loops which are known to be crucial for the
binding and can be used to guide the docking; 2) The detailed steps to perform
docking with the HADDOCK 2.4 webserver following different strategies depending
on the availability of information about epitope residues.