CDR search

Search CDRs based on specific criteria.

1. Get all CDR structures in STCRDab.
2. Get the CDR loops of a particular PDB in STCRDab.

3. Apply an advanced search of CDR structures.






4. Search for unique CDR structures.



The canonical forms of the CDRs were first introduced for antibodies and later for TCRs by Al-Lazikani et al. (2000). Since then, clusters were also identified by Klausen et al. (2015) using the method proposed by North et al. (2011). Here we use the length-independent clustering method (DBSCAN) by Nowak et al. (2016) to identify the canonical forms, and relate them to previous results. The consensus sequence is based on the amino acid conservation in unique sequences of the cluster, where

  • An upper case letter indicates that the amino acid has ≥90% conservation.
  • A lower case letter indicates that the amino acid has 20-90% conservation.

Canonical formConsensus SequenceView representative LoopNumber of loopsal-Lazikani et al. formKlausen et al. formSearch
A1-5-Attfns2vlkD74A1-1Search similar structures
A1-6-BssgnPy1lp9L76A1-2A1-3Search similar structures
A1-6-Cvsgfng5u17B141A1-4Search similar structures
A1-6-Adsasqy4x6bC152A1-1A1-2Search similar structures
A1-7-BTISGndY4ozhE38A1-6Search similar structures
A1-7-ATsdssYg2ak4D20A1-7Search similar structures
A2-5-BGLknN3kpsD36Search similar structures
A2-5-AiaSGT4e41I41A2-1Search similar structures
A2-6-AiysdGd5u1rD148A2-1A2-3Search similar structures
A2-7-Airsvqre3vxsD91A2-2A2-4Search similar structures
A2-7-Bltsagee5euoG107A2-4A2-5Search similar structures
A2-8-BQgSYdeeN4g9fD20A2-8Search similar structures
A2-8-AYfsGDnlV2oi9B49A2-3A2-6Search similar structures
A3-9-AAantgnqfy4jfeD16A3-2Search similar structures
A3-10,11,12-AAasgdsykli5c0bD172Search similar structures
A3-10-AAvmDsnyqLI5u2vE66A3-3Search similar structures
A3-13-AAVRPlldGsYIPT2bnqD18A3-10Search similar structures
A3-13-BvvgDRGStLGRLy3tvmC64A3-8Search similar structures
B1-5-AmnHdy4pjxF391B1-1B1-1Search similar structures
B1-5-BSGHds5c08E129B1-2Search similar structures
B1-5-CSeHlr3vxsE21Search similar structures
B2-6-ASygvgt3qh3B374B2-1B2-2Search similar structures
B2-6-Bfqneee5c07J150B2-3/B2-4/B2-5Search similar structures
B2-7-ASheGfkA2ij0C19Search similar structures
B3-9-AASgggGTlY3oweO72Search similar structures
B3-10,11,12,13-AASslggdeqy3qeuE148Search similar structures
B3-10,11-AASsdrsgeqy3ta3D99Search similar structures
B3-12-BASSylgntgElf2bnqE31Search similar structures
B3-12-AAssfgdanaeQf2nx5U18Search similar structures
B3-13,14-AASSeavggtgelf5u17E65Search similar structures
B3-14-AASRPGLaagqPEQY3pwpE17Search similar structures