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Figure 2 | BMC Bioinformatics

Figure 2

From: An automated framework for understanding structural variations in the binding grooves of MHC class II molecules

Figure 2

Cladograms based on similarities between binding sites. The cladograms for the whole groove and the P4 sub-pocket level similarities among alleles. The first four characters of the label are the PDB identifier for the structure of the MHC class II molecule. The next group of three letters are the chain identifiers used for the alpha chain, beta chain and peptide, respectively, in the original PDB file (there are only two letters in this group in cases where the peptide has been engineered to be part of one of the MHC chains). The final part of the label indicates which alpha and beta alleles are present in the MHC molecule. Branches associated with diseases are shown in brackets with disease label. Disease names are abbreviated as NL:Narcolepsy, T1D:Type 1 Diabetes, RA:Rheumatoid Arthritis, CD: Coeliac Disease and PTB:Pulmanory tuberculosis. The suffix '+' stands for positive association and '-' for negative association of an allele with disease. (A) The cladogram for the whole groove similarities. (B) The cladogram for the P4 similarities. Different branches are indicated by black diamonds to indicate net clustering.

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