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The complementary determining regions (CDR’s) of antibodies determine the selectivity of the antibody. Every antibody has a light and heavy chain and every chain has three CDR’s, very creatively labeled labelled CDR 1, 2 and 3. Besides the division based on chain type and CDR number, the length of the CDR also varies. In this document, we will dive deeper into the method we developed to find clusters within each chain type, CDR number, CDR length combination (from now on CDR group). Our clusters can aid researchers to gain more insight in how CDR’s work and how they relate to each other, which can assist in drug development and antibody research.
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All the CDR’s were grouped by chain type (light or heavy), CDR number (1, 2 or 3) and CDR length (between 3 and 26), resulting in groups like H1_8 (heavy chain, cdr number 1, length 8). All CDR’s within each group are superposed on each other, where the superpositioning is based on the anchors only. This is done so the structural differences are better detectable and visible, and because the anchors are sequentially and structurally more conserved.
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Note: The CDR group labeling labelling is similar to what Dunbirck did. However, since we use different CDR definitions, our H1_8 doesn’t match their H1-8. |
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We found the following number of cluster clusters of each of the different CDR groups. Per CDR group, the clustering pipeline created a lot of different ways to cluster the group, but we then handpicked the best way.
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Annotation
The clusters are always labeled labelled in order by size. So if a CDR group has 3 clusters, the biggest cluster will be cluster 1 and the smallest will be cluster 3. If there is an “outlier cluster” (which isn’t a real cluster), this one is always annotated as cluster 0.