title: Determinants of Macromolecular Specificity from Proteomics-Derived Peptide Substrate Data.
abstract: 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 protein-protein interfaces.
  
  
  METHODS
  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.
  
  
  CONCLUSIONS
  We discuss here future potential, synergies and needs of the emerging overlap disciplines of proteomics and structure-based modelling.
authors.affiliation: Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.
authors.forename: Julian E
authors.initials: JE
authors.lastname: Fuchs
authors.affiliation: Institute of Molecular Medicine and Cell Research, University of Freiburg, Stefan-Meier- Str. 17, D-79104 Freiburg, Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Schilling
authors.affiliation: Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria.
authors.forename: Klaus R
authors.initials: KR
authors.lastname: Liedl
mesh_terms: D000818:Animals; D001665:Binding Sites; D006801:Humans; D008958:Models, Molecular; D010447:Peptide Hydrolases / Q000737:chemistry / Q000378:metabolism; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D059748:Proteolysis; D020543:Proteome / Q000737:chemistry / Q000378:metabolism; D040901:Proteomics; D013379:Substrate Specificity
chemical_list: D010455:Peptides; D020543:Proteome; D010447:Peptide Hydrolases
keywords: Macromolecular recognition; molecular modelling; peptide binding; protease substrate
  profiling; protein-protein-interface; specificity