Linking evolution of protein structures through fragments

Motivation At present there is no universal understanding of how proteins can change topology during evolution, and how such pathways can be determined in a systematic way. The ability to create links between fold topologies would have important consequences for structural classification, structure prediction and homology modeling. Several methods based on geometrical measures have been proposed to create links between topologies, e.g. [1,2]. It has proven difficult, however, to show the evolutionary relevance of such links. Here we use our previously developped age measure for protein superfamilies [3] to investigate the relationship between structural fragments and protein structure evolution.