PyIgClassify (Last updated on November 1, 2019) is a monthly-updated web server primarily providing the clusters and associated information of the antibody complementarity determining regions (CDRs) in the Protein Data Bank (PDB). The current database contains 3,065 PDB antibody entries. The list of PDB entries can be browsed here.

Antibody CDR conformations have been clustered previously by Chothia, Thornton, and others; with the most recent comprehensive clustering appearing in 1997[1][2]. Since then, there has been an explosion of structures in the PDB. Using a dihedral angle metric and an affinity propagation technique, we have clustered the conformations of each CDR and unique loop length of antibody structures in the PDB, at this time, a total of 115 unique clusters [3]. Please browse the statistics page for more information pertaining to each of these clusters. We believe these clusters and their associated structure and sequence data will lead to field-wide improvements in antibody structure prediction and design.

Citing PyIgClassify

PyIgClassify: a database of antibody CDR structural classifications Jared Adolf-Bryfogle; Qifang Xu; Benjamin North; Andreas Lehmann; Roland L. Dunbrack Jr Nucleic Acids Research 2014; doi: 10.1093/nar/gku1106

References

1. Chothia C, Lesk AM. Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 1987; 196:901-17.
2. Al-Lazikani B, Lesk AM, Chothia C. Standard conformations for the canonical structures of immunoglobulins. J. Mol. Biol. 1997;273:927-48.
3. North, B, Lehmann A, Dunbrack R. A new clustering of antibody CDR loop conformations: J. Mol. Biol. (2011), 406(2): 228-256. pdf