Knowledge-based modeling of peptides at protein interfaces: PiPreD

Bioinformatics. 2015 May 1;31(9):1405-10. doi: 10.1093/bioinformatics/btu838. Epub 2014 Dec 23.


Motivation: 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.

Availability and implementation: Database and accessory scripts and programs are available upon request to the authors or at


Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Databases, Protein
  • Knowledge Bases
  • Models, Molecular*
  • Multiprotein Complexes / chemistry
  • Peptides / chemistry*
  • Protein Binding
  • Protein Interaction Domains and Motifs*
  • Protein Interaction Mapping / methods*
  • Software


  • Multiprotein Complexes
  • Peptides