Using the antibody-antigen binding interface to train image-based deep neural networks for antibody-epitope classification
Fig 13
Using multiple Ab models to account for the CDRs flexibility and variations of side-chain orientation.
(A) Superposition of 3-D models of seven EBOV Abs (ADI-15974, ADI-15756, ADI-15758, ADI-15999, ADI-15820, ADI-15848, ADI-16061) that target the stalk region of EBOV GP. For simplicity, the Abs are represented using grey ribbon models with positively- and negatively-charged residues associated with the CDRs shown with a ‘stick’ representation in blue and red, respectively. The light gray fragments of the ribbon models highlighted the positions of the light-chain CDR3s (CDR3-L), and heavy-chain CDR3s (CDR3-H). (B) Superposition of ten 3-D models of Ab ADI-15974 shown in the same orientation as those in (A) and using the same color scheme. Variations in the PDB templates used by Rosetta Antibody for 3-D models generation can lead to differences in the CDRs, and variations in the fingerprint patterns. In addition, for one of the models, we display the remaining positively- and negatively-charged residues of the Ab using cyan and orange colors, respectively. Note that projections of the latter set of residues may also contribute to the fingerprint patterns. (C) Same models as in panel B viewed using a 90° rotation around the horizontal axis.