In an article published last year in the Journal of Chemical Information and Modeling, scientists lead by Anne Goupil-Lamy presented a computational method to identify the epitope of a rat mGlu5 receptor nanobody. 

Throughout their study, the authors employed Discovery Studio 2022 in multiple stages, including model generation, rigid protein-protein docking, molecular dynamics, binding mutation energy calculations, and aggregation propensity score assessments. 

Initially the authors generated models for the NB5A nanobody and the rat mGlu5 receptor. Following model creation, the authors conducted blind docking experiments to identify the epitope region. Two poses were found to align with biological data, and virtual mutations revealed that only one epitope exhibited a destabilizing effect on nanobody binding when residues were mutated to their human homologues. Molecular dynamics simulations further validated this epitope due to its high stability, as observed through RMSD monitoring. 

The in silico experiments successfully identified the likely epitope, which was subsequently validated through experimental residue mutation and binding assays.

To read the full article please navigate to https://pubs.acs.org/doi/10.1021/acs.jcim.3c01620