Protein–protein interactions can be seen as a hierarchical process occurring at three related levels: proteins bind by means of specific domains, which in turn form interfaces through patches of residues.
Detailed knowledge about which domains and residues are involved in a given interaction has extensive applications to biology, including better understanding of the binding process and more efficient drug/enzyme design.
Alas, most current interaction prediction methods do not identify which parts of a protein actually instantiate an interaction.
Furthermore, they also fail to leverage the hierarchical nature of the problem, ignoring otherwise useful information available at the lower levels; when they do, they do not generate predictions that are guaranteed to be consistent between levels.
Authors: Claudio Saccà, Stefano Teso, Michelangelo Diligenti, Andrea Passerini
Book title: BMC Bioinformatics