Background: Recent advances in proteomics methodologies allow for high throughput
profiling of proteolytic cleavage events. The resulting substrate peptide distributions provide deep insights
in the underlying macromolecular recognition events, as determinants of biomolecular specificity
identified by proteomics approaches may be compared to structure-based analysis of corresponding
Method: Here, we present an overview of experimental and computational methodologies and tools
applied in the area and provide an outlook beyond the protein class of proteases.
Results and Conclusion: We discuss here future potential, synergies and needs of the emerging overlap
disciplines of proteomics and structure-based modelling.