CATH – a hierarchic classification of protein domain structures

1. CATH – a hierarchic classification of protein domain structures Rui Kuang

2. CATH Hierarchy • Class: secondary structure composition and contacts mainly alpha, mainly beta and alpha-beta • Architecture: description of the gross arrangement of secondary structures, independent of connectivity Structures with diverse connectivities but common architecture, such as barrel, sandwich and roll

3. CATH Hierarchy • Topology: fold families similar number and arrangement of secondary structures with the same connectivity links • Homologous superfamily: highly similar structures and functional similarity • Sequence family: significant sequence similarity and thus a high probability of having similar structure/function

4. Example:

5. Class into Architecture • In alpha protein only four-helix bundle architecture is distinguishable. More appropriate to group reflecting combinations of common motifs • The constrains on beta strands to be hydrogen bonded within sheets and sheet-sheet packing make them distinct • Alpha-beta class are more constrained and only has eight architectures.

6. Procedures of building CATH