title: Knowledge-based modeling of peptides at protein interfaces: PiPreD.
abstract: BACKGROUND
  Protein-protein interactions (PPIs) underpin virtually all cellular processes both in health and disease. Modulating the interaction between proteins by means of small (chemical) agents is therefore a promising route for future novel therapeutic interventions. In this context, peptides are gaining momentum as emerging agents for the modulation of PPIs.
  
  
  RESULTS
  We reported a novel computational, structure and knowledge-based approach to model orthosteric peptides to target PPIs: PiPreD. PiPreD relies on a precompiled and bespoken library of structural motifs, iMotifs, extracted from protein complexes and a fast structural modeling algorithm driven by the location of native chemical groups on the interface of the protein target named anchor residues. PiPreD comprehensive and systematically samples the entire interface deriving peptide conformations best suited for the given region on the protein interface. PiPreD complements the existing technologies and provides new solutions for the disruption of selected interactions.
  
  
  METHODS
  Database and accessory scripts and programs are available upon request to the authors or at http://www.bioinsilico.org/PIPRED.
  
  
  BACKGROUND
  narcis.fernandez@gmail.com.
authors.affiliation: Structural Bioinformatics Lab (GRIB), Departament de Ciencies Experimental i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain.
authors.forename: Baldo
authors.initials: B
authors.lastname: Oliva
authors.affiliation: Structural Bioinformatics Lab (GRIB), Departament de Ciencies Experimental i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain.
authors.forename: Narcis
authors.initials: N
authors.lastname: Fernandez-Fuentes
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D051188:Knowledge Bases; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D025941:Protein Interaction Mapping / Q000379:methods*; D012984:Software
chemical_list: D046912:Multiprotein Complexes; D010455:Peptides